Maintainer: ‘John R. Stevens <john.r.stevens@usu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("John", "R."),
                      family = "Stevens",
                      role = c("aut", "cre"),
                      email = "john.r.stevens@usu.edu"),
               person(given = c("Todd", "R."),
                      family = "Jones",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Running examples in ‘SigTree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adonis.tree
> ### Title: Function to perform adonis test of independence on p-values from
> ###   tests of multiple OTUs.
> ### Aliases: adonis.tree
> ### Keywords: tree adonis
> 
> ### ** Examples
> 
> ### To access the tutorial document for this package, type in R (not run here): 
> # vignette('SigTree')
> 
> ### Create tree, then data frame, then use plotSigTree to plot the tree
> ### Code for random tree and data frame
> node.size <- 10
> seed <- 109
> # Create tree
> set.seed(seed);
> library(ape)
> r.tree <- rtree(node.size)
> # Create p-values data frame
> set.seed(seed)
> r.pval <- rbeta(node.size, .1, .1)
> # Randomize the order of the tip labels
> # (just to emphasize that labels need not be sorted)
> set.seed(seed)
> r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label))
> r.pvalues <- data.frame(label=r.tip.label, pval=r.pval)
> 
> # Check for dependence among p-values; lack of significance here
> # indicates default test="Stouffer" would be appropriate in other 
> # main SigTree package functions (plotSigTree, export.figtree, 
> # and export.inherit); otherwise, test="Hartung" would be more 
> # appropriate.
> adonis.tree(r.tree,r.pvalues)
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis.tree -> adonis -> .Defunct
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SigTree.Rnw’ using Sweave
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’

Error: processing vignette 'SigTree.Rnw' failed with diagnostics:
 chunk 6 
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").

--- failed re-building ‘SigTree.Rnw’

SUMMARY: processing the following file failed:
  ‘SigTree.Rnw’

Error: Vignette re-building failed.
Execution halted
Maintainer: ‘John R. Stevens <john.r.stevens@usu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("John", "R."),
                      family = "Stevens",
                      role = c("aut", "cre"),
                      email = "john.r.stevens@usu.edu"),
               person(given = c("Todd", "R."),
                      family = "Jones",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Running examples in ‘SigTree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adonis.tree
> ### Title: Function to perform adonis test of independence on p-values from
> ###   tests of multiple OTUs.
> ### Aliases: adonis.tree
> ### Keywords: tree adonis
> 
> ### ** Examples
> 
> ### To access the tutorial document for this package, type in R (not run here): 
> # vignette('SigTree')
> 
> ### Create tree, then data frame, then use plotSigTree to plot the tree
> ### Code for random tree and data frame
> node.size <- 10
> seed <- 109
> # Create tree
> set.seed(seed);
> library(ape)
> r.tree <- rtree(node.size)
> # Create p-values data frame
> set.seed(seed)
> r.pval <- rbeta(node.size, .1, .1)
> # Randomize the order of the tip labels
> # (just to emphasize that labels need not be sorted)
> set.seed(seed)
> r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label))
> r.pvalues <- data.frame(label=r.tip.label, pval=r.pval)
> 
> # Check for dependence among p-values; lack of significance here
> # indicates default test="Stouffer" would be appropriate in other 
> # main SigTree package functions (plotSigTree, export.figtree, 
> # and export.inherit); otherwise, test="Hartung" would be more 
> # appropriate.
> adonis.tree(r.tree,r.pvalues)
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis.tree -> adonis -> .Defunct
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SigTree.Rnw’ using Sweave
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’

Error: processing vignette 'SigTree.Rnw' failed with diagnostics:
 chunk 6 
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").

--- failed re-building ‘SigTree.Rnw’

SUMMARY: processing the following file failed:
  ‘SigTree.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘SigTree-Ex.R’ failed
The error most likely occurred in:

> ### Name: adonis.tree
> ### Title: Function to perform adonis test of independence on p-values from
> ###   tests of multiple OTUs.
> ### Aliases: adonis.tree
> ### Keywords: tree adonis
> 
> ### ** Examples
> 
> ### To access the tutorial document for this package, type in R (not run here): 
> # vignette('SigTree')
> 
> ### Create tree, then data frame, then use plotSigTree to plot the tree
> ### Code for random tree and data frame
> node.size <- 10
> seed <- 109
> # Create tree
> set.seed(seed);
> library(ape)
> r.tree <- rtree(node.size)
> # Create p-values data frame
> set.seed(seed)
> r.pval <- rbeta(node.size, .1, .1)
> # Randomize the order of the tip labels
> # (just to emphasize that labels need not be sorted)
> set.seed(seed)
> r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label))
> r.pvalues <- data.frame(label=r.tip.label, pval=r.pval)
> 
> # Check for dependence among p-values; lack of significance here
> # indicates default test="Stouffer" would be appropriate in other 
> # main SigTree package functions (plotSigTree, export.figtree, 
> # and export.inherit); otherwise, test="Hartung" would be more 
> # appropriate.
> adonis.tree(r.tree,r.pvalues)
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis.tree -> adonis -> .Defunct
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘SigTree.Rnw’ using Sweave
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’

Error: processing vignette 'SigTree.Rnw' failed with diagnostics:
 chunk 6 
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").

--- failed re-building ‘SigTree.Rnw’

SUMMARY: processing the following file failed:
  ‘SigTree.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘SigTree-Ex.R’ failed
The error most likely occurred in:

> ### Name: adonis.tree
> ### Title: Function to perform adonis test of independence on p-values from
> ###   tests of multiple OTUs.
> ### Aliases: adonis.tree
> ### Keywords: tree adonis
> 
> ### ** Examples
> 
> ### To access the tutorial document for this package, type in R (not run here): 
> # vignette('SigTree')
> 
> ### Create tree, then data frame, then use plotSigTree to plot the tree
> ### Code for random tree and data frame
> node.size <- 10
> seed <- 109
> # Create tree
> set.seed(seed);
> library(ape)
> r.tree <- rtree(node.size)
> # Create p-values data frame
> set.seed(seed)
> r.pval <- rbeta(node.size, .1, .1)
> # Randomize the order of the tip labels
> # (just to emphasize that labels need not be sorted)
> set.seed(seed)
> r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label))
> r.pvalues <- data.frame(label=r.tip.label, pval=r.pval)
> 
> # Check for dependence among p-values; lack of significance here
> # indicates default test="Stouffer" would be appropriate in other 
> # main SigTree package functions (plotSigTree, export.figtree, 
> # and export.inherit); otherwise, test="Hartung" would be more 
> # appropriate.
> adonis.tree(r.tree,r.pvalues)
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis.tree -> adonis -> .Defunct
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘SigTree.Rnw’ using Sweave
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’

Error: processing vignette 'SigTree.Rnw' failed with diagnostics:
 chunk 6 
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").

--- failed re-building ‘SigTree.Rnw’

SUMMARY: processing the following file failed:
  ‘SigTree.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in 'SigTree-Ex.R' failed
The error most likely occurred in:

> ### Name: adonis.tree
> ### Title: Function to perform adonis test of independence on p-values from
> ###   tests of multiple OTUs.
> ### Aliases: adonis.tree
> ### Keywords: tree adonis
> 
> ### ** Examples
> 
> ### To access the tutorial document for this package, type in R (not run here): 
> # vignette('SigTree')
> 
> ### Create tree, then data frame, then use plotSigTree to plot the tree
> ### Code for random tree and data frame
> node.size <- 10
> seed <- 109
> # Create tree
> set.seed(seed);
> library(ape)
> r.tree <- rtree(node.size)
> # Create p-values data frame
> set.seed(seed)
> r.pval <- rbeta(node.size, .1, .1)
> # Randomize the order of the tip labels
> # (just to emphasize that labels need not be sorted)
> set.seed(seed)
> r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label))
> r.pvalues <- data.frame(label=r.tip.label, pval=r.pval)
> 
> # Check for dependence among p-values; lack of significance here
> # indicates default test="Stouffer" would be appropriate in other 
> # main SigTree package functions (plotSigTree, export.figtree, 
> # and export.inherit); otherwise, test="Hartung" would be more 
> # appropriate.
> adonis.tree(r.tree,r.pvalues)
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis.tree -> adonis -> .Defunct
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SigTree.Rnw' using Sweave
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'

Error: processing vignette 'SigTree.Rnw' failed with diagnostics:
 chunk 6 
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").

--- failed re-building 'SigTree.Rnw'

SUMMARY: processing the following file failed:
  'SigTree.Rnw'

Error: Vignette re-building failed.
Execution halted
Running examples in ‘SigTree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adonis.tree
> ### Title: Function to perform adonis test of independence on p-values from
> ###   tests of multiple OTUs.
> ### Aliases: adonis.tree
> ### Keywords: tree adonis
> 
> ### ** Examples
> 
> ### To access the tutorial document for this package, type in R (not run here): 
> # vignette('SigTree')
> 
> ### Create tree, then data frame, then use plotSigTree to plot the tree
> ### Code for random tree and data frame
> node.size <- 10
> seed <- 109
> # Create tree
> set.seed(seed);
> library(ape)
> r.tree <- rtree(node.size)
> # Create p-values data frame
> set.seed(seed)
> r.pval <- rbeta(node.size, .1, .1)
> # Randomize the order of the tip labels
> # (just to emphasize that labels need not be sorted)
> set.seed(seed)
> r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label))
> r.pvalues <- data.frame(label=r.tip.label, pval=r.pval)
> 
> # Check for dependence among p-values; lack of significance here
> # indicates default test="Stouffer" would be appropriate in other 
> # main SigTree package functions (plotSigTree, export.figtree, 
> # and export.inherit); otherwise, test="Hartung" would be more 
> # appropriate.
> adonis.tree(r.tree,r.pvalues)
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis.tree -> adonis -> .Defunct
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SigTree.Rnw’ using Sweave
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’

Error: processing vignette 'SigTree.Rnw' failed with diagnostics:
 chunk 6 
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").

--- failed re-building ‘SigTree.Rnw’

SUMMARY: processing the following file failed:
  ‘SigTree.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘SigTree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adonis.tree
> ### Title: Function to perform adonis test of independence on p-values from
> ###   tests of multiple OTUs.
> ### Aliases: adonis.tree
> ### Keywords: tree adonis
> 
> ### ** Examples
> 
> ### To access the tutorial document for this package, type in R (not run here): 
> # vignette('SigTree')
> 
> ### Create tree, then data frame, then use plotSigTree to plot the tree
> ### Code for random tree and data frame
> node.size <- 10
> seed <- 109
> # Create tree
> set.seed(seed);
> library(ape)
> r.tree <- rtree(node.size)
> # Create p-values data frame
> set.seed(seed)
> r.pval <- rbeta(node.size, .1, .1)
> # Randomize the order of the tip labels
> # (just to emphasize that labels need not be sorted)
> set.seed(seed)
> r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label))
> r.pvalues <- data.frame(label=r.tip.label, pval=r.pval)
> 
> # Check for dependence among p-values; lack of significance here
> # indicates default test="Stouffer" would be appropriate in other 
> # main SigTree package functions (plotSigTree, export.figtree, 
> # and export.inherit); otherwise, test="Hartung" would be more 
> # appropriate.
> adonis.tree(r.tree,r.pvalues)
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis.tree -> adonis -> .Defunct
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SigTree.Rnw’ using Sweave
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’

Error: processing vignette 'SigTree.Rnw' failed with diagnostics:
 chunk 6 
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").

--- failed re-building ‘SigTree.Rnw’

SUMMARY: processing the following file failed:
  ‘SigTree.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in 'SigTree-Ex.R' failed
The error most likely occurred in:

> ### Name: adonis.tree
> ### Title: Function to perform adonis test of independence on p-values from
> ###   tests of multiple OTUs.
> ### Aliases: adonis.tree
> ### Keywords: tree adonis
> 
> ### ** Examples
> 
> ### To access the tutorial document for this package, type in R (not run here): 
> # vignette('SigTree')
> 
> ### Create tree, then data frame, then use plotSigTree to plot the tree
> ### Code for random tree and data frame
> node.size <- 10
> seed <- 109
> # Create tree
> set.seed(seed);
> library(ape)
> r.tree <- rtree(node.size)
> # Create p-values data frame
> set.seed(seed)
> r.pval <- rbeta(node.size, .1, .1)
> # Randomize the order of the tip labels
> # (just to emphasize that labels need not be sorted)
> set.seed(seed)
> r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label))
> r.pvalues <- data.frame(label=r.tip.label, pval=r.pval)
> 
> # Check for dependence among p-values; lack of significance here
> # indicates default test="Stouffer" would be appropriate in other 
> # main SigTree package functions (plotSigTree, export.figtree, 
> # and export.inherit); otherwise, test="Hartung" would be more 
> # appropriate.
> adonis.tree(r.tree,r.pvalues)
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis.tree -> adonis -> .Defunct
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SigTree.Rnw' using Sweave
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'

Error: processing vignette 'SigTree.Rnw' failed with diagnostics:
 chunk 6 
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").

--- failed re-building 'SigTree.Rnw'

SUMMARY: processing the following file failed:
  'SigTree.Rnw'

Error: Vignette re-building failed.
Execution halted
Running examples in 'SigTree-Ex.R' failed
The error most likely occurred in:

> ### Name: adonis.tree
> ### Title: Function to perform adonis test of independence on p-values from
> ###   tests of multiple OTUs.
> ### Aliases: adonis.tree
> ### Keywords: tree adonis
> 
> ### ** Examples
> 
> ### To access the tutorial document for this package, type in R (not run here): 
> # vignette('SigTree')
> 
> ### Create tree, then data frame, then use plotSigTree to plot the tree
> ### Code for random tree and data frame
> node.size <- 10
> seed <- 109
> # Create tree
> set.seed(seed);
> library(ape)
> r.tree <- rtree(node.size)
> # Create p-values data frame
> set.seed(seed)
> r.pval <- rbeta(node.size, .1, .1)
> # Randomize the order of the tip labels
> # (just to emphasize that labels need not be sorted)
> set.seed(seed)
> r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label))
> r.pvalues <- data.frame(label=r.tip.label, pval=r.pval)
> 
> # Check for dependence among p-values; lack of significance here
> # indicates default test="Stouffer" would be appropriate in other 
> # main SigTree package functions (plotSigTree, export.figtree, 
> # and export.inherit); otherwise, test="Hartung" would be more 
> # appropriate.
> adonis.tree(r.tree,r.pvalues)
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis.tree -> adonis -> .Defunct
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SigTree.Rnw' using Sweave
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by 'S4Vectors'

Error: processing vignette 'SigTree.Rnw' failed with diagnostics:
 chunk 6 
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").

--- failed re-building 'SigTree.Rnw'

SUMMARY: processing the following file failed:
  'SigTree.Rnw'

Error: Vignette re-building failed.
Execution halted