[Phylobase-commits] r875 - pkg/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Mar 17 14:13:03 CET 2014
Author: francois
Date: 2014-03-17 14:13:02 +0100 (Mon, 17 Mar 2014)
New Revision: 875
Modified:
pkg/tests/misctests.R
pkg/tests/misctests.Rout.save
pkg/tests/phylo4dtests.Rout.save
pkg/tests/phylosubtest.Rout.save
pkg/tests/phylotorture.Rout.save
pkg/tests/plottest.Rout.save
pkg/tests/roundtrip.R
pkg/tests/roundtrip.Rout.save
pkg/tests/testprune.Rout.save
Log:
updated tests and output
Modified: pkg/tests/misctests.R
===================================================================
--- pkg/tests/misctests.R 2014-03-17 12:48:09 UTC (rev 874)
+++ pkg/tests/misctests.R 2014-03-17 13:13:02 UTC (rev 875)
@@ -1,97 +1,112 @@
+library(phylobase)
+library(ape)
-R version 3.0.3 (2014-03-06) -- "Warm Puppy"
-Copyright (C) 2014 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+set.seed(1)
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
+data(geospiza)
- Natural language support but running in an English locale
+## make sure geospiza is properly formatted
+if(is.character(checkval <- checkPhylo4(geospiza)))
+ stop(checkval)
+
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
+geospiza0 <-
+ list(geospiza.tree=as(geospiza,"phylo"),geospiza.data=tipData(geospiza))
+## push data back into list form as in geiger
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
+t1 <- try(p1 <- phylo4d(geospiza0$geospiza.tree,geospiza0$geospiza.data))
+## Error in checkData(res, ...) :
+## Tip data names are a subset of tree tip labels.
-> ## RUnit script obtained from:
-> ## http://wiki.r-project.org/rwiki/doku.php?id=developers:runit
->
-> ## unit tests will not be done if RUnit is not available
-> if(require("RUnit", quietly=TRUE)) {
-+
-+ ## --- Setup ---
-+
-+ pkg <- "phylobase"
-+ if(Sys.getenv("RCMDCHECK") == "FALSE") {
-+ ## Path to unit tests for standalone running under Makefile (not R CMD check)
-+ ## PKG/tests/../inst/unitTests
-+ path <- file.path(getwd(), "..", "inst", "unitTests")
-+ } else {
-+ ## Path to unit tests for R CMD check
-+ ## PKG.Rcheck/tests/../PKG/unitTests
-+ path <- system.file(package=pkg, "unitTests")
-+ }
-+ cat("\nRunning unit tests\n")
-+ print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
-+
-+ library(package=pkg, character.only=TRUE)
-+
-+ ## If desired, load the name space to allow testing of private functions
-+ ## if (is.element(pkg, loadedNamespaces()))
-+ ## attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3)
-+ ##
-+ ## or simply call PKG:::myPrivateFunction() in tests
-+
-+ ## --- Testing ---
-+
-+ ## Define tests
-+ testSuite <- defineTestSuite(name=paste(pkg, "unit testing"),
-+ dirs=path)
-+ ## Run
-+ tests <- runTestSuite(testSuite)
-+
-+ ## Default report name
-+ pathReport <- file.path(path, "report")
-+
-+ ## Report to stdout and text files
-+ cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
-+ printTextProtocol(tests, showDetails=FALSE)
-+ printTextProtocol(tests, showDetails=FALSE,
-+ fileName=paste(pathReport, "Summary.txt", sep=""))
-+ printTextProtocol(tests, showDetails=TRUE,
-+ fileName=paste(pathReport, ".txt", sep=""))
-+
-+ ## Report to HTML file
-+ printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
-+
-+ ## Return stop() to cause R CMD check stop in case of
-+ ## - failures i.e. FALSE to unit tests or
-+ ## - errors i.e. R errors
-+ tmp <- getErrors(tests)
-+ if(tmp$nFail > 0 | tmp$nErr > 0) {
-+ stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail,
-+ ", #R errors: ", tmp$nErr, ")\n\n", sep=""))
-+ }
-+ } else {
-+ warning("cannot run unit tests -- package RUnit is not available")
-+ }
+p2 <- as(geospiza0$geospiza.tree,"phylo4")
+plot(p2)
-Running unit tests
-$pkg
-[1] "phylobase"
+lab1 <- tipLabels(p2)
+lab2 <- rownames(geospiza0$geospiza.data)
-$getwd
-[1] "/home/francois/R-dev/phylobase/pkg/tests"
+lab1[!lab1 %in% lab2] ## missing data
+lab2[!lab2 %in% lab1] ## extra data (none)
+p1 <- phylo4d(p2,geospiza0$geospiza.data, missing.data="warn")
+p1 <- phylo4d(p2,geospiza0$geospiza.data, missing.data="OK")
-$pathToUnitTests
-[1] "/home/francois/.R/library/phylobase/unitTests"
+plot(p1)
+plot(p1,show.node.label=TRUE)
+## one way to deal with it:
+p1B <- prune(p1,tip="olivacea")
-Warning messages:
-1: replacing previous import by ‘Rcpp::evalCpp’ when loading ‘phylobase’
-2: replacing previous import by ‘ade4::newick2phylog’ when loading ‘phylobase’
-Execution halted
+## or ...
+p1C <- na.omit(p1)
+
+labels(p1C, "all") <- tolower(labels(p1C, "all"))
+
+## trace("prune",browser,signature="phylo4d")
+r1 <- read.tree(text="((t4:0.3210275554,(t2:0.2724586465,t3:0.2724586465):0.0485689089):0.1397952619,(t5:0.07551818331,t1:0.07551818331):0.385304634);")
+
+## trace("phylo4d", browser, signature = "phylo")
+## untrace("phylo4d", signature = "phylo")
+tipdat <- data.frame(a=1:5, row.names=r1$tip.label)
+q1 <- phylo4d(r1,tip.data=tipdat, node.data=data.frame(a=6:9), match.data=FALSE)
+q2 <- prune(q1,1)
+summary(q2)
+
+tipdat2 <- tipdat
+row.names(tipdat2)[1] <- "s1"
+t1 <- try(q1 <- phylo4d(r1,tip.data=tipdat2))
+
+plot(q2)
+plot(q2,type="cladogram")
+## plot(p2,type="dotchart",labels.nodes=nodeLabels(p2))
+## trace("plot", browser, signature = c("phylo4d","missing"))
+tipLabels(q1) <- paste("q",1:5,sep="")
+nodeLabels(q1) <- paste("n",1:4,sep="")
+p3 <- phylo4d(r1,tip.data=tipdat,node.data=data.frame(b=6:9), match.data=FALSE)
+summary(p3)
+
+plot(p1)
+
+plot(subset(p1,tips.include=c("fuliginosa","fortis","magnirostris",
+ "conirostris","scandens")))
+## better error?
+## Error in phy$edge[, 2] : incorrect number of dimensions
+
+if(dev.cur() == 1) get(getOption("device"))()
+plot(subset(p2,tips.include=c("fuliginosa","fortis","magnirostris",
+ "conirostris","scandens")))
+
+plot(p2,show.node.label=TRUE)
+
+tree.owls <- read.tree(text="(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);")
+
+z <- as(tree.owls,"phylo4")
+
+example("phylo4d")
+obj1 <- obj2 <- obj3 <- phylo4d(z, data.frame(wing=1:4,color=factor(c("b","w","b","b")), tail=runif(4)*10), match.data=FALSE)
+
+obj2 at data <- as.data.frame(obj2 at data[,1])
+obj3 at data <- cbind(obj1 at data,obj2 at data)
+obj4 <- obj1
+obj4 at data[2,3] <- NA
+obj4 at data[1,1] <- NA
+
+nodeLabels(obj4) <- character(0)
+
+obj5 <- obj1
+tipData(obj4) <- subset(tipData(obj4),select=sapply(tipData(obj4),class)=="numeric")
+
+treePlot(obj4)
+
+E <- matrix(c(
+ 8, 9,
+ 9, 10,
+ 10, 1,
+ 10, 2,
+ 9, 3,
+ 9, 4,
+ 8, 11,
+ 11, 5,
+ 11, 6,
+ 11, 7,
+ 0, 8), ncol=2,byrow=TRUE)
+
+P2 <- phylo4(E)
Modified: pkg/tests/misctests.Rout.save
===================================================================
--- pkg/tests/misctests.Rout.save 2014-03-17 12:48:09 UTC (rev 874)
+++ pkg/tests/misctests.Rout.save 2014-03-17 13:13:02 UTC (rev 875)
@@ -1,8 +1,7 @@
-R Under development (unstable) (2012-11-20 r61133) -- "Unsuffered Consequences"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
-Platform: i686-pc-linux-gnu (32-bit)
+R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -20,16 +19,14 @@
> library(phylobase)
Loading required package: grid
-Loading required package: ape
-Loading required package: Rcpp
+> library(ape)
-Attaching package: ‘phylobase’
+Attaching package: ‘ape’
-The following object is masked from ‘package:ape’:
+The following object is masked from ‘package:phylobase’:
edges
-> library(ape)
>
> set.seed(1)
>
@@ -189,7 +186,7 @@
phyl4d> treeOwls <- "((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3);"
-phyl4d> tree.owls.bis <- read.tree(text=treeOwls)
+phyl4d> tree.owls.bis <- ape::read.tree(text=treeOwls)
phyl4d> try(phylo4d(as(tree.owls.bis,"phylo4"),data.frame(wing=1:3)), silent=TRUE)
label node ancestor edge.length node.type wing
@@ -414,12 +411,10 @@
26 N26 26 25 0.05167 internal <NA>
27 N27 27 26 0.01500 internal <NA>
-phyl4d> require(ape) ## for rcoal
-
phyl4d> ## generate a tree and some data
phyl4d> set.seed(1)
-phyl4d> p3 <- rcoal(5)
+phyl4d> p3 <- ape::rcoal(5)
phyl4d> dat <- data.frame(a = rnorm(5), b = rnorm(5), row.names = p3$tip.label)
@@ -497,4 +492,4 @@
>
> proc.time()
user system elapsed
- 3.260 2.556 5.671
+ 8.550 0.204 8.738
Modified: pkg/tests/phylo4dtests.Rout.save
===================================================================
--- pkg/tests/phylo4dtests.Rout.save 2014-03-17 12:48:09 UTC (rev 874)
+++ pkg/tests/phylo4dtests.Rout.save 2014-03-17 13:13:02 UTC (rev 875)
@@ -1,8 +1,7 @@
-R Under development (unstable) (2012-11-20 r61133) -- "Unsuffered Consequences"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
-Platform: i686-pc-linux-gnu (32-bit)
+R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -20,16 +19,14 @@
> library(phylobase)
Loading required package: grid
-Loading required package: ape
-Loading required package: Rcpp
+> library(ape)
-Attaching package: ‘phylobase’
+Attaching package: ‘ape’
-The following object is masked from ‘package:ape’:
+The following object is masked from ‘package:phylobase’:
edges
-> require(ape)
> tree.phylo <- read.tree(text="(((A,B)C,D),E);") #only one node is labelled
> tree <- as(tree.phylo, "phylo4")
>
@@ -92,4 +89,4 @@
>
> proc.time()
user system elapsed
- 1.908 2.216 3.978
+ 5.490 0.101 5.564
Modified: pkg/tests/phylosubtest.Rout.save
===================================================================
--- pkg/tests/phylosubtest.Rout.save 2014-03-17 12:48:09 UTC (rev 874)
+++ pkg/tests/phylosubtest.Rout.save 2014-03-17 13:13:02 UTC (rev 875)
@@ -1,8 +1,7 @@
-R Under development (unstable) (2012-11-20 r61133) -- "Unsuffered Consequences"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
-Platform: i686-pc-linux-gnu (32-bit)
+R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -18,15 +17,13 @@
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
-> require(phylobase)
-Loading required package: phylobase
+> library(phylobase)
Loading required package: grid
-Loading required package: ape
-Loading required package: Rcpp
+> library(ape)
-Attaching package: ‘phylobase’
+Attaching package: ‘ape’
-The following object is masked from ‘package:ape’:
+The following object is masked from ‘package:phylobase’:
edges
@@ -47,4 +44,4 @@
>
> proc.time()
user system elapsed
- 1.704 2.288 3.855
+ 5.208 0.106 5.285
Modified: pkg/tests/phylotorture.Rout.save
===================================================================
--- pkg/tests/phylotorture.Rout.save 2014-03-17 12:48:09 UTC (rev 874)
+++ pkg/tests/phylotorture.Rout.save 2014-03-17 13:13:02 UTC (rev 875)
@@ -18,12 +18,9 @@
Type 'q()' to quit R.
> ## torture-testing phylo4 objects.
-> require(phylobase)
-Loading required package: phylobase
+> library(phylobase)
Loading required package: grid
-Loading required package: Rcpp
-> require(ape)
-Loading required package: ape
+> library(ape)
Attaching package: ‘ape’
@@ -31,26 +28,23 @@
edges
-> set.seed(1001)
-> p1 <- list()
-> n <- 10
+>
+> set.seed(10101)
+> n <- 200
+> p1 <- vector("list", n)
> ## don't want to slow down R CMD check by doing this every time:
> ## n <- 10000
> for (i in 1:n) {
-+ ## e2 <- c(sample(1:5,replace=FALSE,size=5),sample(6:10,replace=FALSE,size=5))
-+ ## e1 <- sample(6:10,replace=TRUE
-+ e <- matrix(sample(1:10,replace=TRUE,size=10),ncol=2)
-+ p1[[i]] <- try(phylo4(e),silent=TRUE)
++ if (i <= n/2) {
++ e <- matrix(sample(1:10, replace=TRUE, size=10), ncol=2)
++ }
++ else {
++ e <- cbind(sample(rep(11:19, 2)), sample(1:19))
++ e <- rbind(c(0, sample(11:19, 1)), e)
++ }
++ 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.
+There were 50 or more warnings (use warnings() to see the first 50)
> 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:
@@ -61,14 +55,20 @@
'names' attribute [2] must be the same length as the vector [1]
Error in .local(x, ...) : Nodes incorrectly labeled.
+> unname(table(sapply(p1[!OKvals], as.character)))
+[1] 3 53 44
+> if (sum(OKvals)) message("There are ", sum(OKvals), " valid trees...")
+There are 100 valid trees...
>
> if (any(OKvals)) {
+ p2 <- p1[OKvals]
+ length(p2)
-+ has.poly <- sapply(p2,hasPoly)
-+ has.sing <- sapply(p2,hasSingle)
-+ has.retic <- sapply(p2,hasRetic)
-+ ##
++ has.poly <- sapply(p2, hasPoly)
++ has.sing <- sapply(p2, hasSingle)
++ has.retic <- sapply(p2, hasRetic)
++ message("number of trees with polytomies: ", sum(has.poly))
++ message("number of trees with singletons: ", sum(has.sing))
++ message("number of trees with reticulation: ", sum(has.retic))
+ if (any(has.sing)) {
+ p4 <- p2[has.sing]
+ plot(p4[[1]]) ## gives descriptive error
@@ -82,6 +82,9 @@
+ ## plot(p2[[13]])
+ }
+ }
+number of trees with polytomies: 100
+number of trees with singletons: 0
+number of trees with reticulation: 100
>
> ## elements 8 and 34 are
> ## what SHOULD the rules for trees be?
@@ -135,19 +138,14 @@
> ## 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.>
+> message(try(as(broke2, "phylo4"), silent=TRUE))
+Error in .createLabels(value = tip.label, ntips = ntips, nnodes = nnodes, :
+ Number of labels does not match number of nodes.
+
> ## error regarding number of tip labels vs edges and nodes
-> print(try(phylo4(broke2$edge), silent=TRUE))
-[1] "Error in .local(x, ...) : Nodes incorrectly labeled. \n"
-attr(,"class")
-[1] "try-error"
-attr(,"condition")
-<simpleError in .local(x, ...): Nodes incorrectly labeled. >
+> message(try(phylo4(broke2$edge), silent=TRUE))
+Error in .local(x, ...) : Nodes incorrectly labeled.
+
>
> # switch root node value (6) with next internal node (7):
>
@@ -181,31 +179,22 @@
> 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$edge),silent=TRUE)) # error message saying tree has more than one root
-[1] "Error in .local(x, ...) : Nodes incorrectly labeled. \n"
-attr(,"class")
-[1] "try-error"
-attr(,"condition")
-<simpleError in .local(x, ...): Nodes incorrectly labeled. >
+> message(try(as(broke4, "phylo4"), silent=TRUE))
+Error in .local(x, ...) : Nodes incorrectly labeled.
+
+> message(try(phylo4(broke4$edge), silent=TRUE))
+Error 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)))
+> message(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.>
+Error in treePlot(x, ...) : treePlot function requires a rooted tree.
+
>
> foo at label <- c(rep('blah',10), rep("",9))
>
@@ -214,9 +203,9 @@
> ## 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)
+> 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
+ 6.842 0.111 6.930
Modified: pkg/tests/plottest.Rout.save
===================================================================
--- pkg/tests/plottest.Rout.save 2014-03-17 12:48:09 UTC (rev 874)
+++ pkg/tests/plottest.Rout.save 2014-03-17 13:13:02 UTC (rev 875)
@@ -1,8 +1,7 @@
-R Under development (unstable) (2012-11-20 r61133) -- "Unsuffered Consequences"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
-Platform: i686-pc-linux-gnu (32-bit)
+R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -20,16 +19,14 @@
> library(phylobase)
Loading required package: grid
-Loading required package: ape
-Loading required package: Rcpp
+> library(ape)
-Attaching package: ‘phylobase’
+Attaching package: ‘ape’
-The following object is masked from ‘package:ape’:
+The following object is masked from ‘package:phylobase’:
edges
-> ## library(ape)
>
> data(geospiza)
> g1 <- as(geospiza,"phylo4")
@@ -87,4 +84,4 @@
>
> proc.time()
user system elapsed
- 2.136 2.312 4.300
+ 6.264 0.102 6.336
Modified: pkg/tests/roundtrip.R
===================================================================
--- pkg/tests/roundtrip.R 2014-03-17 12:48:09 UTC (rev 874)
+++ pkg/tests/roundtrip.R 2014-03-17 13:13:02 UTC (rev 875)
@@ -1,4 +1,5 @@
library(phylobase)
+library(ape)
## set.seed(1)
## t0A <- rcoal(5)
Modified: pkg/tests/roundtrip.Rout.save
===================================================================
--- pkg/tests/roundtrip.Rout.save 2014-03-17 12:48:09 UTC (rev 874)
+++ pkg/tests/roundtrip.Rout.save 2014-03-17 13:13:02 UTC (rev 875)
@@ -1,8 +1,7 @@
-R Under development (unstable) (2012-11-19 r61131) -- "Unsuffered Consequences"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
-Platform: i686-pc-linux-gnu (32-bit)
+R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -20,12 +19,11 @@
> library(phylobase)
Loading required package: grid
-Loading required package: ape
-Loading required package: Rcpp
+> library(ape)
-Attaching package: ‘phylobase’
+Attaching package: ‘ape’
-The following object is masked from ‘package:ape’:
+The following object is masked from ‘package:phylobase’:
edges
@@ -79,4 +77,4 @@
>
> proc.time()
user system elapsed
- 1.252 1.692 2.908
+ 5.491 0.205 5.671
Modified: pkg/tests/testprune.Rout.save
===================================================================
--- pkg/tests/testprune.Rout.save 2014-03-17 12:48:09 UTC (rev 874)
+++ pkg/tests/testprune.Rout.save 2014-03-17 13:13:02 UTC (rev 875)
@@ -1,8 +1,7 @@
-R Under development (unstable) (2012-11-20 r61133) -- "Unsuffered Consequences"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
-Platform: i686-pc-linux-gnu (32-bit)
+R version 3.0.3 (2014-03-06) -- "Warm Puppy"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -20,16 +19,14 @@
> library(phylobase)
Loading required package: grid
-Loading required package: ape
-Loading required package: Rcpp
+> library(ape)
-Attaching package: ‘phylobase’
+Attaching package: ‘ape’
-The following object is masked from ‘package:ape’:
+The following object is masked from ‘package:phylobase’:
edges
-> library(ape)
>
> set.seed(1)
> r1 <- rcoal(5)
@@ -86,4 +83,4 @@
>
> proc.time()
user system elapsed
- 1.852 2.220 3.939
+ 5.442 0.090 5.550
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