Errors in running code in vignettes:
when running code in ‘SNPtools.Rnw’
  ...

> library(SNPtools)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: Rsamtools

> snp.file = "http://cgd.jax.org/tools/SNPtools/Build38/sanger.snps.NCBI38.txt.gz"

> mgi.file = "http://cgd.jax.org/tools/SNPtools/MGI/MGI.20130305.sorted.txt.gz"

> available.strains = get.strains(snp.file)

> strains = available.strains[c(4, 2, 8, 15, 16, 10, 
+     17, 18)]

> strains
[1] "A/J"         "129S1/SvImJ" "C57BL/6J"    "NOD/ShiLtJ"  "NZO/HlLtJ"  
[6] " CAST/EiJ"   "PWK/PhJ"     "WSB/EiJ"    

> data(qtl)

> head(qtl)
  Chromosome Position       lod
1          1  3252796 0.9701113
2          1  3336839 0.9658992
3          1  3668628 0.9190987
4          1  3977130 0.8604857
5          1  4430623 0.8551462
6          1  4531029 0.7322654

> cat.snps = variant.plot(var.file = snp.file, mgi.file = mgi.file, 
+     chr = 7, start = 103.3, end = 104.3, strains = strains, pattern = strains[c .... [TRUNCATED] 
[1] "Checking arguments..."
[1] "Retreiving Variants..."
[1] "25450 Variants in region."
[1] "Getting SNPs that match the pattern..."
[1] "2751 variants fit the pattern."
[1] "Categorizing pattern variants..."
[1] "19 genes have variants that fit the pattern between the 3'UTR and the 5'UTR (including introns)."
[1] "Getting genes in region..."
[1] "66 genes in region."
[1] "Drawing plot..."

> head(cat.snps)
              ID CHROM       POS REF ALT symbol   id       type
5037  rs49176439     7 103499458   C   A   <NA> <NA> intergenic
6312           .     7 103544588   G A,C   <NA> <NA> intergenic
7199           .     7 103579635   T   C   <NA> <NA> intergenic
9107  rs45805035     7 103661698   T   C   <NA> <NA> intergenic
9110  rs47660696     7 103661709   A   G   <NA> <NA> intergenic
9111 rs215837914     7 103661720   G   T   <NA> <NA> intergenic

> available.strains = get.strains(snp.file)

> strains = available.strains[c(4, 2, 8, 15, 16, 10, 
+     17, 18)]

> snps = get.variants(chr = 7, start = 103.3, end = 104.3, 
+     strains = strains, type = "snp")

> nrow(snps)
[1] 25394

> nsnps = convert.variants.to.numeric(snps)

> snp.plot(nsnps, ref = "C57BL/6J", cluster = T)

> strain.subset = c("C57BL/6J", "NOD/ShiLtJ", "NZO/HlLtJ")

> snp.subset = get.pattern.variants(snps, strain.subset)

> nrow(snp.subset)
[1] 2596

> snp.plot(nsnps, ref = "C57BL/6J", cluster = T, highlight = strain.subset, 
+     pattern = snp.subset)

> data(qtl)

> head(qtl)
  Chromosome Position       lod
1          1  3252796 0.9701113
2          1  3336839 0.9658992
3          1  3668628 0.9190987
4          1  3977130 0.8604857
5          1  4430623 0.8551462
6          1  4531029 0.7322654

> snp.plot(nsnps, ref = "C57BL/6J", cluster = T, highlight = strain.subset, 
+     pattern = snp.subset, qtl = qtl)

> mgi = get.mgi.features(chr = 7, start = 103, end = 105, 
+     source = "MGI", type = "gene")

> mgi = mgi[-grep("^Gm", mgi$Name), ]

> snp.plot(nsnps, ref = "C57BL/6J", cluster = T, highlight = strain.subset, 
+     pattern = snp.subset, qtl = qtl, mgi = mgi)

> snps = get.variants(chr = 7, start = 103.3, end = 104.3, 
+     strains = strains, type = "snp")

  When sourcing ‘SNPtools.R’:
Error: read line failed (error code 4); corrupt or invalid file?
Execution halted