Errors in running code in vignettes:
when running code in 'methodComparison.Rnw'

> options(keep.source = TRUE, width = 60)

> packageInfo <- packageDescription("vipor")

> library(vipor)

> packageKeywords <- "visualization, display, one dimensional, grouped, groups, violin, scatter, points, quasirandom, beeswarm, van der Corput, beanpl ..." ... [TRUNCATED] 

> library(vipor)

> library(beeswarm)

  When sourcing 'methodComparison.R':
Error: there is no package called 'beeswarm'
Execution halted
when running code in 'usageExamples.Rnw'

> options(keep.source = TRUE, width = 60)

> packageInfo <- packageDescription("vipor")

> library(vipor)

> packageKeywords <- "visualization, display, one dimensional, grouped, groups, violin, scatter, points, quasirandom, beeswarm, van der Corput"

> library(vipor)

> set.seed(12345)

> n <- 100

> dat <- rnorm(n * 2)

> labs <- rep(c("a", "b"), n)

> vpPlot(labs, dat)

> vpPlot(labs, dat, las = 1, ylab = "Data", col = rep(1:2, 
+     n))

> abline(h = 0, lty = 2)

> labs2 <- factor(labs, levels = c("b", "a"))

> vpPlot(labs2, dat, las = 1, ylab = "Data", col = rep(1:2, 
+     n))

> abline(h = 0, lty = 2)

> offsets <- offsetX(dat, labs)

> head(offsets, 4)
[1] -0.18939738  0.10387013  0.28854590  0.01104955

> xPos <- vpPlot(labs, dat)

> head(xPos, 4)
[1] 0.8106026 2.1038701 1.2885459 2.0110496

> xPos2 <- rep(1:2, n) + offsets

> head(xPos2, 4)
[1] 0.8106026 2.1038701 1.2885459 2.0110496

> all(xPos == xPos2)
[1] TRUE

> dat <- list(Normal = rnorm(50), `Dense normal` = rnorm(500), 
+     Bimodal = c(rnorm(100), rnorm(100, 5)), Extremes = rcauchy(100))

> par(mfrow = c(4, 1), mar = c(2.5, 3.1, 1.2, 0.5), 
+     mgp = c(2.1, 0.75, 0), cex.axis = 1.2, cex.lab = 1.2, cex.main = 1.2)

> dummy <- sapply(names(dat), function(label) {
+     y <- dat[[label]]
+     offsets <- list(defaults = offsetX(y), `adjust=2` = offsetX(y, 
+        .... [TRUNCATED] 

> dat <- list(`10 points` = rnorm(10), `50 points` = rnorm(50, 
+     2), `200 points` = c(rnorm(400), rnorm(100, 5)), `5000 points` = rnorm(5000, 
+  .... [TRUNCATED] 

> labs <- rep(names(dat), sapply(dat, length))

> labs <- factor(labs, levels = unique(labs))

> vpPlot(labs, unlist(dat), offsetXArgs = list(varwidth = TRUE), 
+     las = 1, ylab = "Value", col = "#00000066", bg = "#00000022", 
+     pch = 21)

> y <- c(beaver1$temp, beaver2$temp)

> x <- rep(c("Beaver 1", "Beaver 2"), c(nrow(beaver1), 
+     nrow(beaver2)))

> vpPlot(x, y, las = 1, ylab = "Body temperature", pch = 21, 
+     col = "#00000099", bg = "#00000033")

> ints <- integrations[integrations$nearestGene > 0, 
+     ]

> y <- log(ints$nearestGene)

> x <- as.factor(paste(ints$study, ints$latent))

> activeCols <- c(Expressed = "#FF000033", Unexpressed = "#0000FF33")

> cols <- activeCols[ints$latent]

> par(mar = c(4, 7, 0.1, 0.1))

> vpPlot(x, y, las = 2, ylab = "Log distance to gene", 
+     xaxt = "n", pch = 21, col = cols, bg = cols, cex = 0.7)

> uniqX <- levels(x)

> prettyX <- tapply(1:length(uniqX), sub("(Une|E)xpressed$", 
+     "", uniqX), mean)

> axis(1, prettyX, names(prettyX), las = 2)

> legend(grconvertX(0.01, from = "ndc"), grconvertY(0.15, 
+     from = "ndc"), names(activeCols), pch = 21, col = cols, pt.bg = activeCols, 
+     xp .... [TRUNCATED] 

> library(ggbeeswarm)

  When sourcing 'usageExamples.R':
Error: there is no package called 'ggbeeswarm'
Execution halted

  'methodComparison.Rnw'... failed
  'usageExamples.Rnw'... failed