Running examples in ‘mvabund-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.mvabund
> ### Title: Plot Multivariate Abundance Data and Formulae
> ### Aliases: plot.mvabund plot.mvformula
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 
> require(graphics)
> 
> ############################
> ## Some "type (1)" plots ##
> ############################
> 
> data(solberg)
> solbdat <- solberg$abund
> treatment<- solberg$x
> 
> ## Plot a multivariate dataset (Species vs Abundance)
> plot.mvabund(solbdat)
Kicking off BoxPlot sequence 
Overlapping points were shifted along the y-axis to make them visible.


ABOUT TO PLOT THE FUNCTION 

Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot 
(the variables with highest total abundance).
> 
> ## Alternatively, the plot command could be used directly if spiddat is 
> ## defined as an mvabund object:
> solbmvabund <- mvabund(solbdat)
> plot(solbmvabund)
Kicking off BoxPlot sequence 
Overlapping points were shifted along the y-axis to make them visible.


ABOUT TO PLOT THE FUNCTION 

Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot 
(the variables with highest total abundance).
> 
> ## Draw an mvabund object in a boxplot, but using the 20 most abundant 
> ## variables in the plot, using the square root transform, and adding 
> ## coloured axes and title:
> plot.mvabund(solbdat, n.vars=20, type="bx", transformation="sqrt", 
+ fg="lightblue", main="Solberg abundances", col.main="red")
Kicking off BoxPlot sequence 
Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata, Dichromadora_sp., Neochromadora_sp., Richtersia_inaequalis, Pandolaimus_latilaimus, Leptolaimus_elegans, Halalaimus_sp., Desmolaimus_sp., Linhomieidae_un.A were included in the plot 
(the variables with highest total abundance).
> 
> ## Plot Species (split by treatment) vs Abundance
> plot(solbmvabund,treatment)
Overlapping points were shifted along the y-axis to make them visible.

 PIPING TO 1st MVFACTOR 
Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot 
(the variables with highest total abundance).
> 
> ## This can also be produced using
> plot(solbmvabund~treatment)
Overlapping points were shifted along the y-axis to make them visible.

 PIPING TO 2nd MVFACTOR 
Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot 
(the variables with highest total abundance).
> 
> ## To use plot.mvabund to plot only the variables with P-values less than 0.1:
> lm.solberg <- manylm(log(solbmvabund+1)~treatment)
> anova.solb <- anova(lm.solberg, p.uni="unadjusted")
> pj = anova.solb$uni.p
> 
> plot(solbmvabund~treatment, var.subset=pj<0.1)
Overlapping points were shifted along the y-axis to make them visible.

 PIPING TO 2nd MVFACTOR 
Only the variables Viscosia_sp., Prochromadorella_sp., Daptonema_sp.1, Sphaerolaimus_macrocirculus were included in the plot (user selected).
> 
> ## Or to plot only the 12 most significant variables, according to their 
> ## univariate ANOVA P-values:
> pj.sort = sort(pj, index.return=TRUE)
> plot(solbmvabund~treatment, var.subset=pj.sort$ix[1:12])
Overlapping points were shifted along the y-axis to make them visible.

 PIPING TO 2nd MVFACTOR 
Only the variables Daptonema_sp.1, Viscosia_sp., Sphaerolaimus_macrocirculus, Prochromadorella_sp., Dichromadora_sp., Odontophora_sp., Pandolaimus_latilaimus, Terschellingia_longicaudata, Cyatholaimidae_un., Sabatieria_punctata, Halichoanolaimus_dolichurus, Sabatieria_sp. were included in the plot (user selected).
> 
> 
> ############################
> ## Some "type (2)" plots ##
> ############################
> #load and convert data
> data(spider)
> spiddat <- mvabund(spider$abund)
> spidx <- mvabund(spider$x)
> 
> #create labels vectors
> pch.vec <- as.numeric(spidx[,3]<2)
> pch.vec[pch.vec==0] <- 3
> 
> #Scale the soil water variable
> soilWater <- spidx[,1]
> 
> #Create the Table for the main titles of each plot
> title <- c("\n\nAlopecosa accentuata", "\n\nAlopecosa cuneata",
+            "\n\nAlopecosa fabrilis", "\n\nArctosa lutetiana", 
+            "\n\nArctosa perita", "\n\nAulonia albimana", 
+            "\n\nPardosa lugubris", "\n\nPardosa monticola", 
+            "\n\nPardosa nigriceps", "\n\nPardosa pullata",
+            "\n\nTrochosa terricola", "\n\nZora spinimana")
> 
> #Plot Species Abundance vs Environmental variable
> plot.mvformula(log(spiddat+1) ~ exp(soilWater), main=title, 
+ xlab="% Soil Moist - Log Scale  ", ylab="Abundance [log scale]", 
+ overall.main="Species Abundance vs %Soil Moisture", col=pch.vec, 
+ fg="grey", pch=pch.vec, las=1, scale.lab="ss",t.lab="o", mfrow=c(4,3),log="x")

 	PIPING TO 2nd PLOT FORMULA FEATURE 
plot 2
Warning in plot.window(...) :
  "transformation.formula" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "transformation.formula" is not a graphical parameter
Warning in title(...) :
  "transformation.formula" is not a graphical parameter

 *** caught segfault ***
address 0x53, cause 'memory not mapped'

Traceback:
 1: mtext(overall.main, outer = TRUE, cex = 0.9 * par("cex.main"),     col = par("col.main"), line = 1)
 2: default.plot.mvformula(x, y = NA, type = type, n.vars = n.vars,     var.subset = var.subset, xvar.select = xvar.select, n.xvars = n.xvars,     xvar.subset = xvar.subset, transformation.formula = transformation,     ...)
 3: plot.mvformula(log(spiddat + 1) ~ exp(soilWater), main = title,     xlab = "% Soil Moist - Log Scale  ", ylab = "Abundance [log scale]",     overall.main = "Species Abundance vs %Soil Moisture", col = pch.vec,     fg = "grey", pch = pch.vec, las = 1, scale.lab = "ss", t.lab = "o",     mfrow = c(4, 3), log = "x")
An irrecoverable exception occurred. R is aborting now ...