Hi I'm encountered the following error while reading a vcf file using the motifbreakR package.

vcf <- "/Users/asd2007/Tools/vcftools/examples/annotate-test.vcf"
vars <- snps.from.file(file =vcf, search.genome = BSgenome.Hsapiens.UCSC.hg19, format = "vcf")

Error: 'seqlevels<-' is not an exported object from 'namespace:VariantAnnotation'

I am able to read this vcf using succesfully with the following line: 

readVcf(vcf, "hg19") 

However, it is not immediately obvious to me whether motifbreakR would accept this format.

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] VariantAnnotation_1.16.1          Rsamtools_1.22.0                  SummarizedExperiment_1.0.0        Biobase_2.30.0                    BSgenome.Hsapiens.UCSC.hg19_1.4.0
 [6] motifbreakR_1.0.0                 MotifDb_1.12.0                    BSgenome_1.38.0                   rtracklayer_1.30.1                Biostrings_2.38.0                
[11] XVector_0.10.0                    GenomicRanges_1.22.0              GenomeInfoDb_1.6.0                IRanges_2.4.1                     S4Vectors_0.8.0                  
[16] BiocGenerics_0.16.0              

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1               locfit_1.5-9.1            biovizBase_1.18.0         lattice_0.20-33           digest_0.6.8              plyr_1.8.3                futile.options_1.0.0     
 [8] acepack_1.3-3.3           RSQLite_1.0.0             ggplot2_1.0.1.9003        MotIV_1.26.0              zlibbioc_1.16.0           GenomicFeatures_1.22.0    annotate_1.48.0          
[15] rpart_4.1-10              proto_0.3-10              splines_3.2.2             BiocParallel_1.4.0        stringr_1.0.0             geneplotter_1.48.0        foreign_0.8-66           
[22] RCurl_1.95-4.7            biomaRt_2.26.0            munsell_0.4.2             compiler_3.2.2            seqLogo_1.36.0            Gviz_1.14.0               nnet_7.3-11              
[29] gridExtra_2.0.0           Hmisc_3.17-0              matrixStats_0.15.0        XML_3.98-1.3              TFMPvalue_0.0.5           GenomicAlignments_1.6.1   bitops_1.0-6             
[36] xtable_1.7-4              gtable_0.1.2              DBI_0.3.1                 magrittr_1.5              scales_0.3.0              stringi_1.0-1             genefilter_1.52.0        
[43] RcppArmadillo_0.6.100.0.0 ggthemes_2.2.1            latticeExtra_0.6-26       futile.logger_1.4.1       grImport_0.9-0            Formula_1.2-1             rGADEM_2.18.0            
[50] lambda.r_1.1.7            RColorBrewer_1.1-2        tools_3.2.2               dichromat_2.0-0           ade4_1.7-2                DESeq2_1.10.0             survival_2.38-3          
[57] AnnotationDbi_1.32.0      colorspace_1.2-6          cluster_2.0.3             motifStack_1.14.0        


> BiocInstaller::biocValid()

* sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] VariantAnnotation_1.16.1          Rsamtools_1.22.0                  SummarizedExperiment_1.0.0        Biobase_2.30.0                    BSgenome.Hsapiens.UCSC.hg19_1.4.0
 [6] motifbreakR_1.0.0                 MotifDb_1.12.0                    BSgenome_1.38.0                   rtracklayer_1.30.1                Biostrings_2.38.0                
[11] XVector_0.10.0                    GenomicRanges_1.22.0              GenomeInfoDb_1.6.0                IRanges_2.4.1                     S4Vectors_0.8.0                  
[16] BiocGenerics_0.16.0              

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1               locfit_1.5-9.1            biovizBase_1.18.0         lattice_0.20-33           digest_0.6.8              plyr_1.8.3                futile.options_1.0.0     
 [8] acepack_1.3-3.3           RSQLite_1.0.0             BiocInstaller_1.20.0      ggplot2_1.0.1.9003        MotIV_1.26.0              zlibbioc_1.16.0           GenomicFeatures_1.22.0   
[15] annotate_1.48.0           rpart_4.1-10              proto_0.3-10              splines_3.2.2             BiocParallel_1.4.0        stringr_1.0.0             geneplotter_1.48.0       
[22] foreign_0.8-66            RCurl_1.95-4.7            biomaRt_2.26.0            munsell_0.4.2             compiler_3.2.2            seqLogo_1.36.0            Gviz_1.14.0              
[29] nnet_7.3-11               gridExtra_2.0.0           Hmisc_3.17-0              matrixStats_0.15.0        XML_3.98-1.3              TFMPvalue_0.0.5           GenomicAlignments_1.6.1  
[36] bitops_1.0-6              xtable_1.7-4              gtable_0.1.2              DBI_0.3.1                 magrittr_1.5              scales_0.3.0              stringi_1.0-1            
[43] genefilter_1.52.0         RcppArmadillo_0.6.100.0.0 ggthemes_2.2.1            latticeExtra_0.6-26       futile.logger_1.4.1       grImport_0.9-0            Formula_1.2-1            
[50] rGADEM_2.18.0             lambda.r_1.1.7            RColorBrewer_1.1-2        tools_3.2.2               dichromat_2.0-0           ade4_1.7-2                DESeq2_1.10.0            
[57] survival_2.38-3           AnnotationDbi_1.32.0      colorspace_1.2-6          cluster_2.0.3             motifStack_1.14.0        

* Packages too new for Bioconductor version '3.2'

        Version      LibPath                                                         
ggplot2 "1.0.1.9003" "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"

downgrade with biocLite("ggplot2")

Yes, there was a problem in the snps.from.file function. Thanks for the extra eyes. Fixed it up, it should be in the next build of the package, 1.0.1, tomorrow. Or you can get it from github now.