Error in re-building vignettes:
  ...
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 4.8-1).
Type 'help("meta-package")' for a brief overview.
Warning in var(var1, na.rm = TRUE) :
  Calling var(x) on a factor x is deprecated and will become an error.
  Use something like 'all(duplicated(x)[-1L])' to test for a constant vector.
Warning in var(var1, na.rm = TRUE) :
  Calling var(x) on a factor x is deprecated and will become an error.
  Use something like 'all(duplicated(x)[-1L])' to test for a constant vector.
Warning in max(abs(as.vector(res[, snpinds, , 1]))[pvs < 0.05], na.rm = T) :
  no non-missing arguments to max; returning -Inf
Warning in .manhattan(topl, logfun, beta1 = NULL, paste(opts$mPhen.title,  :
  NAs introduced by coercion
Warning in var(var1, na.rm = TRUE) :
  Calling var(x) on a factor x is deprecated and will become an error.
  Use something like 'all(duplicated(x)[-1L])' to test for a constant vector.
Warning in var(var1, na.rm = TRUE) :
  Calling var(x) on a factor x is deprecated and will become an error.
  Use something like 'all(duplicated(x)[-1L])' to test for a constant vector.
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "MultiPhen.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : 
  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'MultiPhen'. The following files exist in directory '.': 'ALL.chr21.integrated.phase1.v3.20101123.snps.indels.svs.genotypes.extract.impute', 'ALL.chr21.integrated.phase1.v3.20101123.snps.indels.svs.genotypes.extract.vcf.gz', 'ALL.chr21.integrated.phase1.v3.20101123.snps.indels.svs.genotypes.extract.zip', 'ALL.chr21.integrated_phase1_v3.20101123.snps_indels_svs.genotypes_extract.impute', 'ALL.chr21.integrated_phase1_v3.20101123.snps_indels_svs.genotypes_extract.vcf.gz', 'ALL.chr21.integrated_phase1_v3.20101123.snps_indels_svs.genotypes_extract.zip', 'MultiPhen.Rnw', 'MultiPhen.tex', 'Rplots.pdf', 'hapmap2.bed', 'hapmap2.bim', 'hapmap2.fam', 'pheno.txt'
Calls: buildVignettes -> find_vignette_product
Execution halted