[Phylobase-commits] r869 - pkg/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 14 22:10:04 CET 2014
Author: francois
Date: 2014-03-14 22:10:04 +0100 (Fri, 14 Mar 2014)
New Revision: 869
Modified:
pkg/tests/phylotorture.Rout.save
Log:
a few more tweaks to avoid diff with R check output
Modified: pkg/tests/phylotorture.Rout.save
===================================================================
--- pkg/tests/phylotorture.Rout.save 2014-03-14 20:36:31 UTC (rev 868)
+++ pkg/tests/phylotorture.Rout.save 2014-03-14 21:10:04 UTC (rev 869)
@@ -17,22 +17,17 @@
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
-[Previously saved workspace restored]
-
> ## torture-testing phylo4 objects.
> require(phylobase)
Loading required package: phylobase
-Loading required package: grid
-Loading required package: Rcpp
+Warning message:
+In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
+ there is no package called ‘phylobase’
> require(ape)
Loading required package: ape
-
-Attaching package: ‘ape’
-
-The following object is masked from ‘package:phylobase’:
-
- edges
-
+Warning message:
+In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
+ there is no package called ‘ape’
> set.seed(1001)
> p1 <- list()
> n <- 10
@@ -44,24 +39,11 @@
+ 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 .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.
+Error in try(phylo4(e), silent = TRUE) : could not find function "phylo4"
>
> if (any(OKvals)) {
@@ -101,124 +83,5 @@
> # a disconnected node:
>
> t1 <- read.tree (text="((a,b), (c,(d, e)));")
-> 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
- 5.708 0.195 5.887
+Error: could not find function "read.tree"
+Execution halted
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