[Phylobase-commits] r870 - pkg/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 14 23:56:06 CET 2014
Author: francois
Date: 2014-03-14 23:56:05 +0100 (Fri, 14 Mar 2014)
New Revision: 870
Modified:
pkg/tests/phylotorture.Rout.save
Log:
previous commit was wrong output file
Modified: pkg/tests/phylotorture.Rout.save
===================================================================
--- pkg/tests/phylotorture.Rout.save 2014-03-14 21:10:04 UTC (rev 869)
+++ pkg/tests/phylotorture.Rout.save 2014-03-14 22:56:05 UTC (rev 870)
@@ -20,14 +20,17 @@
> ## torture-testing phylo4 objects.
> require(phylobase)
Loading required package: phylobase
-Warning message:
-In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
- there is no package called ‘phylobase’
+Loading required package: grid
+Loading required package: Rcpp
> require(ape)
Loading required package: ape
-Warning message:
-In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
- there is no package called ‘ape’
+
+Attaching package: ‘ape’
+
+The following object is masked from ‘package:phylobase’:
+
+ edges
+
> set.seed(1001)
> p1 <- list()
> n <- 10
@@ -39,11 +42,24 @@
+ e <- matrix(sample(1:10,replace=TRUE,size=10),ncol=2)
+ p1[[i]] <- try(phylo4(e),silent=TRUE)
+ }
+Warning messages:
+1: In checkTree(object) : Tree contains singleton nodes.
+2: In checkTree(object) : Tree contains singleton nodes.
+3: In checkTree(object) : Tree contains singleton nodes.
+4: In checkTree(object) : Tree contains singleton nodes.
+5: In checkTree(object) : Tree contains singleton nodes.
+6: In checkTree(object) : Tree contains singleton nodes.
+7: In checkTree(object) : Tree contains singleton nodes.
+8: In checkTree(object) : Tree contains singleton nodes.
> OKvals <- sapply(p1, class) != "try-error"
> ## table(sapply(p1[!OKvals], as.character)) # I think this is causing issues with
> ## R check because of different width of terminal/output, trying something simpler:
> message(unique(sapply(p1[!OKvals], as.character)))
-Error in try(phylo4(e), silent = TRUE) : could not find function "phylo4"
+Error in .local(x, ...) :
+ Tips incorrectly labeled. Nodes incorrectly labeled.
+Error in names(res) <- switch(type, tip = 1:ntips, internal = seq(from = ntips + :
+ 'names' attribute [2] must be the same length as the vector [1]
+Error in .local(x, ...) : Nodes incorrectly labeled.
>
> if (any(OKvals)) {
@@ -83,5 +99,124 @@
> # a disconnected node:
>
> t1 <- read.tree (text="((a,b), (c,(d, e)));")
-Error: could not find function "read.tree"
-Execution halted
+> plot(t1)
+>
+> broke1 <- t1
+> broke1$edge[broke1$edge[,2] ==9, 1] <- 9 # disconnect the node, two subtrees, ((a, b), c) and (d,e)
+>
+> try(as(broke1, "phylo4") -> tree, silent=TRUE) # makes a phylo4 object with no warning
+Warning messages:
+1: In checkTree(object) : Tree contains singleton nodes.
+2: In checkTree(object) : Tree contains singleton nodes.
+3: In checkTree(object) : Tree contains singleton nodes.
+> try(phylo4(broke1$edge), silent=TRUE) # constructor makes a phylo4 object with no warning
+ label node ancestor edge.length node.type
+1 T1 1 7 NA tip
+2 T2 2 7 NA tip
+3 T3 3 8 NA tip
+4 T4 4 9 NA tip
+5 T5 5 9 NA tip
+6 <NA> 6 0 NA internal
+7 <NA> 7 6 NA internal
+8 <NA> 8 6 NA internal
+9 <NA> 9 9 NA internal
+Warning messages:
+1: In checkTree(object) : Tree contains singleton nodes.
+2: In checkTree(object) : Tree contains singleton nodes.
+> ## error message comes from ape, not phylo? -- AND
+> ## error is about singles, not disconnected nodes
+> ## print(try(plot(tree), silent=TRUE )) ## pdc couldn't get this to work, so temporarily commenting
+>
+> # root node value != ntips + 1:
+>
+> broke2 <- t1
+> broke2$edge[broke2$edge==6] <- 10
+>
+> ## warning, but no error
+> ## plot(broke2) ## seems to hang R CMD check??
+> ## generates error, but it's about wrong number of tips, not wrong value at root.
+> print(try(as(broke2, "phylo4"), silent=TRUE))
+[1] "Error in .createLabels(value = tip.label, ntips = ntips, nnodes = nnodes, : \n Number of labels does not match number of nodes.\n"
+attr(,"class")
+[1] "try-error"
+attr(,"condition")
+<simpleError in .createLabels(value = tip.label, ntips = ntips, nnodes = nnodes, type = "tip"): Number of labels does not match number of nodes.>
+> ## error regarding number of tip labels vs edges and nodes
+> print(try(phylo4(broke2$edge), silent=TRUE))
+[1] "Error in .local(x, ...) : Nodes incorrectly labeled. \n"
+attr(,"class")
+[1] "try-error"
+attr(,"condition")
+<simpleError in .local(x, ...): Nodes incorrectly labeled. >
+>
+> # switch root node value (6) with next internal node (7):
+>
+> broke3 <- broke2
+> broke3$edge[broke3$edge==7] <- 6
+> broke3$edge[broke3$edge==10] <- 7
+>
+> ## both of the following now fail with
+> ## "root node is not at position (nTips+1)
+> try(as(broke3,"phylo4") -> tree3) # works with no error message
+> try(phylo4(broke3$edge)) # works with no error message
+ label node ancestor edge.length node.type
+1 T1 1 6 NA tip
+2 T2 2 6 NA tip
+3 T3 3 8 NA tip
+4 T4 4 9 NA tip
+5 T5 5 9 NA tip
+6 <NA> 6 7 NA internal
+7 <NA> 7 0 NA internal
+8 <NA> 8 7 NA internal
+9 <NA> 9 8 NA internal
+> ## plot(tree3) # would work if we could create it?
+>
+>
+> # tips have larger numbers than root node:
+>
+> broke4 <- t1
+> broke4$edge[broke4$edge==1] <- 11
+> broke4$edge[broke4$edge==2] <- 12
+> broke4$edge[broke4$edge==3] <- 13
+> broke4$edge[broke4$edge==4] <- 14
+> broke4$edge[broke4$edge==5] <- 15
+>
+> print(try(as(broke4, "phylo4"), silent=TRUE) ) # error message saying tree has more than one root
+[1] "Error in .local(x, ...) : Nodes incorrectly labeled. \n"
+attr(,"class")
+[1] "try-error"
+attr(,"condition")
+<simpleError in .local(x, ...): Nodes incorrectly labeled. >
+> print(try(phylo4(broke4$edge),silent=TRUE)) # error message saying tree has more than one root
+[1] "Error in .local(x, ...) : Nodes incorrectly labeled. \n"
+attr(,"class")
+[1] "try-error"
+attr(,"condition")
+<simpleError in .local(x, ...): Nodes incorrectly labeled. >
+> # print(try(plot(broke4), TRUE)) ## CAUSES R TO HANG!
+>
+> ###
+> foo <- new('phylo4')
+> set.seed(1001)
+> foo at edge <- rcoal(10)$edge
+> print(try(plot(foo)))
+Error in treePlot(x, ...) : treePlot function requires a rooted tree.
+[1] "Error in treePlot(x, ...) : treePlot function requires a rooted tree.\n"
+attr(,"class")
+[1] "try-error"
+attr(,"condition")
+<simpleError in treePlot(x, ...): treePlot function requires a rooted tree.>
+>
+> foo at label <- c(rep('blah',10), rep("",9))
+>
+> #####
+> ## tree with only 2 tips: will fail under previous versions
+> ## with "Error in if (which(nAncest == 0) != nTips + 1) { :
+> ## argument is of length zero"
+>
+> edge <- matrix(c(3,1,3,2),byrow=TRUE,ncol=2)
+> try(p2 <- phylo4(edge), silent=TRUE)
+>
+> proc.time()
+ user system elapsed
+ 5.557 0.099 5.638
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