[Phylobase-commits] r830 - pkg/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Mar 24 21:01:23 CET 2011
Author: francois
Date: 2011-03-24 21:01:22 +0100 (Thu, 24 Mar 2011)
New Revision: 830
Removed:
pkg/tests/RUnit-tests.R
pkg/tests/RUnit-tests.Rout.save
Modified:
pkg/tests/doRUnit.Rout.save
Log:
deleted old RUnit files, updated output of doRUnit.R
Deleted: pkg/tests/RUnit-tests.R
===================================================================
--- pkg/tests/RUnit-tests.R 2011-03-21 14:31:47 UTC (rev 829)
+++ pkg/tests/RUnit-tests.R 2011-03-24 20:01:22 UTC (rev 830)
@@ -1,7 +0,0 @@
-require(RUnit)
-## TODO -- find solution to run these tests on R-forge
-
-##testsuite <- defineTestSuite("phylobase", dirs="/home/francois/Work/R-dev/phylobase/branches/fm-branch/RUnit-tests",
-## testFileRegexp="^test", testFuncRegexp="^test")
-##testRslt <- runTestSuite(testsuite)
-##printTextProtocol(testRslt)
Deleted: pkg/tests/RUnit-tests.Rout.save
===================================================================
--- pkg/tests/RUnit-tests.Rout.save 2011-03-21 14:31:47 UTC (rev 829)
+++ pkg/tests/RUnit-tests.Rout.save 2011-03-24 20:01:22 UTC (rev 830)
@@ -1,32 +0,0 @@
-
-R version 2.12.0 (2010-10-15)
-Copyright (C) 2010 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
-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.
-Type 'license()' or 'licence()' for distribution details.
-
- Natural language support but running in an English locale
-
-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.
-
-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.
-
-> require(RUnit)
-Loading required package: RUnit
-> ## TODO -- find solution to run these tests on R-forge
->
-> ##testsuite <- defineTestSuite("phylobase", dirs="/home/francois/Work/R-dev/phylobase/branches/fm-branch/RUnit-tests",
-> ## testFileRegexp="^test", testFuncRegexp="^test")
-> ##testRslt <- runTestSuite(testsuite)
-> ##printTextProtocol(testRslt)
->
-> proc.time()
- user system elapsed
- 0.34 0.02 0.36
Modified: pkg/tests/doRUnit.Rout.save
===================================================================
--- pkg/tests/doRUnit.Rout.save 2011-03-21 14:31:47 UTC (rev 829)
+++ pkg/tests/doRUnit.Rout.save 2011-03-24 20:01:22 UTC (rev 830)
@@ -1,6 +1,6 @@
-R version 2.12.0 (2010-10-15)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R version 2.12.2 (2011-02-25)
+Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -8,8 +8,6 @@
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
- Natural language support but running in an English locale
-
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.
@@ -86,10 +84,10 @@
[1] "phylobase"
$getwd
-[1] "/home/francois/R-dev/phylobase/pkg/tests"
+[1] "/home/francois/R-dev/phylobase/pkg.Rcheck/tests"
$pathToUnitTests
-[1] "/home/francois/.R/library/phylobase/unitTests"
+[1] "/home/francois/R-dev/phylobase/pkg.Rcheck/phylobase/unitTests"
Loading required package: grid
Loading required package: ape
@@ -111,6 +109,24 @@
+Executing test function test.phylo4.matrix ... Error in .createLabels(value = tip.label, ntips = ntips, nnodes = nnodes, :
+ Number of labels does not match number of nodes.
+Error in .createLabels(node.label, ntips = ntips, nnodes = nnodes, type = "internal") :
+ Number of labels does not match number of nodes.
+Error in .local(x, ...) :
+ unknown order: allowed values are unknown,preorder,postorder,pruningwise,cladewise
+Error in checkSlotAssignment(object, name, value) :
+ assignment of an object of class "character" is not valid for slot "annote" in an object of class "phylo4"; is(value, "list") is not TRUE
+ done successfully.
+
+
+
+Executing test function test.phylo4.phylo ... Error in .local(x, ...) : Labels are not unique
+Error in .local(x, ...) : Labels are not unique
+ done successfully.
+
+
+
Executing test function test.phylo4d.matrix ... done successfully.
@@ -136,24 +152,6 @@
-Executing test function test.phylo4.matrix ... Error in .createLabels(value = tip.label, ntips = ntips, nnodes = nnodes, :
- Number of labels does not match number of nodes.
-Error in .createLabels(node.label, ntips = ntips, nnodes = nnodes, type = "internal") :
- Number of labels does not match number of nodes.
-Error in .local(x, ...) :
- unknown order: allowed values are unknown,preorder,postorder,pruningwise,cladewise
-Error in checkSlotAssignment(object, name, value) :
- assignment of an object of class "character" is not valid for slot "annote" in an object of class "phylo4"; is(value, "list") is not TRUE
- done successfully.
-
-
-
-Executing test function test.phylo4.phylo ... Error in .local(x, ...) : Labels are not unique
-Error in .local(x, ...) : Labels are not unique
- done successfully.
-
-
-
Executing test function test.formatData ... Error in formatData(phy.alt, phy.alt) :
phy.alt must be a vector, factor, matrix, or data frame
Error : label.column %in% 1:ncol(dt) is not TRUE
@@ -182,9 +180,7 @@
-Executing test function test.formatDataWithDup ... [1] 10
-<environment: 0x20e0660>
-Error in formatData(phy.dup, phy.dup) :
+Executing test function test.formatDataWithDup ... Error in formatData(phy.dup, phy.dup) :
phy.dup must be a vector, factor, matrix, or data frame
Error in formatData(phy.dup, data.frame(a = 1:5, row.names = c(rev(lab.tip)[1:3], :
The following nodes are not found in the dataset: t1, t1
@@ -214,95 +210,125 @@
-Executing test function test.addData.phylo4 ... done successfully.
+Executing test function test.Replace.edgeLabels.phylo4 ... Error in .createEdge(value, x at edge, type = "labels") :
+ Names provided don't match internal edge labels names.
+Error in .createEdge(value, x at edge, type = "labels") :
+ Names provided don't match internal edge labels names.
+ done successfully.
-Executing test function test.addData.phylo4d ... done successfully.
+Executing test function test.Replace.edgeLength.phylo4 ... Error in .createEdge(value, x at edge, type = "lengths", use.names) :
+ Names provided don't match internal edge labels names.
+Error in .createEdge(value, x at edge, type = "lengths", use.names) :
+ Names provided don't match internal edge labels names.
+Error in .local(x, ..., value = value) : NAs in edge lengths
+ done successfully.
-Executing test function test.hasNodeData.phylo4d ... done successfully.
+Executing test function test.Replace.labels.phylo4 ... Error in `labels<-`(`*tmp*`, value = structure(c("t2", "t2", "t3", "t4", :
+ Labels are not unique
+Error in `labels<-`(`*tmp*`, value = structure(c("t1", "t2", "t3", "t4", :
+ Labels are not unique
+Error in .createLabels(value, nTips(x), nNodes(x), use.names, type = type) :
+ Number of labels does not match number of nodes.
+Error in .createLabels(value, nTips(x), nNodes(x), use.names, type = type) :
+ Number of labels does not match number of nodes.
+ done successfully.
-Executing test function test.na.omit.phylo4d ... done successfully.
+Executing test function test.Replace.nodeLabels.phylo4 ... Error in `labels<-`(`*tmp*`, type = "internal", ..., value = structure(c("n7", :
+ Labels are not unique
+Error in .createLabels(value, nTips(x), nNodes(x), use.names, type = type) :
+ Number of labels does not match number of nodes.
+Error in .createLabels(value, nTips(x), nNodes(x), use.names, type = type) :
+ Number of labels does not match number of nodes.
+ done successfully.
-Executing test function test.nData ... done successfully.
+Executing test function test.Replace.rootNode.phylo4 ... done successfully.
-Executing test function test.nodeData.phylo4d ... done successfully.
+Executing test function test.Replace.tipLabels.phylo4 ... Error in `labels<-`(`*tmp*`, type = "tip", ..., value = structure(c("t2", :
+ Labels are not unique
+Error in .createLabels(value, nTips(x), nNodes(x), use.names, type = type) :
+ Number of labels does not match number of nodes.
+Error in .createLabels(value, nTips(x), nNodes(x), use.names, type = type) :
+ Number of labels does not match number of nodes.
+ done successfully.
-Executing test function test.Replace.nodeData.phylo4d ... done successfully.
+Executing test function test.depthTips.phylo4 ... done successfully.
-Executing test function test.Replace.tdata.phylo4d ... done successfully.
+Executing test function test.edgeId.phylo4 ... done successfully.
-Executing test function test.Replace.tipData.phylo4d ... done successfully.
+Executing test function test.edgeLabels.phylo4 ... done successfully.
-Executing test function test.summary.phylo4d ... done successfully.
+Executing test function test.edgeLength.phylo4 ... done successfully.
-Executing test function test.tdata.phylo4d ... done successfully.
+Executing test function test.edgeOrder.phylo4 ... done successfully.
-Executing test function test.tipData.phylo4d ... done successfully.
+Executing test function test.edges.phylo4 ... done successfully.
-Executing test function test.edgeId.phylo4 ... done successfully.
+Executing test function test.hasEdgeLabels.phylo4 ... done successfully.
-Executing test function test.edgeLabels.phylo4 ... done successfully.
+Executing test function test.hasEdgeLength.phylo4 ... done successfully.
-Executing test function test.edgeLength.phylo4 ... done successfully.
+Executing test function test.hasNodeLabels.phylo4 ... done successfully.
-Executing test function test.edgeOrder.phylo4 ... done successfully.
+Executing test function test.head.phylo4 ... done successfully.
-Executing test function test.edges.phylo4 ... done successfully.
+Executing test function test.isRooted.phylo4 ... done successfully.
-Executing test function test.hasEdgeLabels.phylo4 ... done successfully.
+Executing test function test.isUltrametric ... Error in isUltrametric(tmpPhy) : The tree has no edge lengths.
+ done successfully.
-Executing test function test.hasEdgeLength.phylo4 ... done successfully.
+Executing test function test.labels.phylo4 ... done successfully.
-Executing test function test.hasNodeLabels.phylo4 ... done successfully.
+Executing test function test.nEdges.phylo4 ... done successfully.
-Executing test function test.head.phylo4 ... done successfully.
+Executing test function test.nNodes.phylo4 ... done successfully.
-Executing test function test.isRooted.phylo4 ... done successfully.
+Executing test function test.nTips.ANY ... done successfully.
-Executing test function test.labels.phylo4 ... done successfully.
+Executing test function test.nTips.phylo4 ... done successfully.
@@ -310,14 +336,10 @@
-Executing test function test.nEdges.phylo4 ... done successfully.
+Executing test function test.nodeDepth.phylo4 ... done successfully.
-Executing test function test.nNodes.phylo4 ... done successfully.
-
-
-
Executing test function test.nodeId.phylo4 ... done successfully.
@@ -330,91 +352,78 @@
-Executing test function test.nTips.ANY ... done successfully.
+Executing test function test.reorder.phylo4 ... done successfully.
-Executing test function test.nTips.phylo4 ... done successfully.
+Executing test function test.rootNode.phylo4 ... done successfully.
-Executing test function test.reorder.phylo4 ... done successfully.
+Executing test function test.sumEdgeLength.phylo4 ... done successfully.
-Executing test function test.Replace.edgeLabels.phylo4 ... Error in .createEdge(value, x at edge, type = "labels") :
- Names provided don't match internal edge labels names.
-Error in .createEdge(value, x at edge, type = "labels") :
- Names provided don't match internal edge labels names.
- done successfully.
+Executing test function test.summary.phylo4 ... done successfully.
-Executing test function test.Replace.edgeLength.phylo4 ... Error in .createEdge(value, x at edge, type = "lengths", use.names) :
- Names provided don't match internal edge labels names.
-Error in .createEdge(value, x at edge, type = "lengths", use.names) :
- Names provided don't match internal edge labels names.
-Error in .local(x, ..., value = value) : NAs in edge lengths
- done successfully.
+Executing test function test.tail.phylo4 ... done successfully.
-Executing test function test.Replace.labels.phylo4 ... Error in `labels<-`(`*tmp*`, value = structure(c("t2", "t2", "t3", "t4", :
- Labels are not unique
-Error in `labels<-`(`*tmp*`, value = structure(c("t1", "t2", "t3", "t4", :
- Labels are not unique
-Error in .createLabels(value, nTips(x), nNodes(x), use.names, type = type) :
- Number of labels does not match number of nodes.
-Error in .createLabels(value, nTips(x), nNodes(x), use.names, type = type) :
- Number of labels does not match number of nodes.
- done successfully.
+Executing test function test.tipLabels.phylo4 ... done successfully.
-Executing test function test.Replace.nodeLabels.phylo4 ... Error in `labels<-`(`*tmp*`, type = "internal", ..., value = structure(c("n7", :
- Labels are not unique
-Error in .createLabels(value, nTips(x), nNodes(x), use.names, type = type) :
- Number of labels does not match number of nodes.
-Error in .createLabels(value, nTips(x), nNodes(x), use.names, type = type) :
- Number of labels does not match number of nodes.
- done successfully.
+Executing test function test.Replace.nodeData.phylo4d ... done successfully.
-Executing test function test.Replace.rootNode.phylo4 ... done successfully.
+Executing test function test.Replace.tdata.phylo4d ... done successfully.
-Executing test function test.Replace.tipLabels.phylo4 ... Error in `labels<-`(`*tmp*`, type = "tip", ..., value = structure(c("t2", :
- Labels are not unique
-Error in .createLabels(value, nTips(x), nNodes(x), use.names, type = type) :
- Number of labels does not match number of nodes.
-Error in .createLabels(value, nTips(x), nNodes(x), use.names, type = type) :
- Number of labels does not match number of nodes.
- done successfully.
+Executing test function test.Replace.tipData.phylo4d ... done successfully.
-Executing test function test.rootNode.phylo4 ... done successfully.
+Executing test function test.addData.phylo4 ... done successfully.
-Executing test function test.sumEdgeLength.phylo4 ... done successfully.
+Executing test function test.addData.phylo4d ... done successfully.
-Executing test function test.summary.phylo4 ... done successfully.
+Executing test function test.hasNodeData.phylo4d ... done successfully.
-Executing test function test.tail.phylo4 ... done successfully.
+Executing test function test.nData ... done successfully.
-Executing test function test.tipLabels.phylo4 ... done successfully.
+Executing test function test.na.omit.phylo4d ... done successfully.
+Executing test function test.nodeData.phylo4d ... done successfully.
+
+
+
+Executing test function test.summary.phylo4d ... done successfully.
+
+
+
+Executing test function test.tdata.phylo4d ... done successfully.
+
+
+
+Executing test function test.tipData.phylo4d ... done successfully.
+
+
+
Executing test function test.assign.pdata ... done successfully.
@@ -440,10 +449,10 @@
Executing test function test.phylobase.options ... Error in match.arg(foo, c("warn", "fail", "ok")) :
- 'arg' should be one of “warn”, “fail”, “ok”
-Error in phylobase.options(1) : invalid argument: ‘1’
+ 'arg' should be one of "warn", "fail", "ok"
+Error in phylobase.options(1) : invalid argument: '1'
Error in phylobase.options(foobar = "foo") :
- Option name invalid: ‘foobar’
+ Option name invalid: 'foobar'
done successfully.
@@ -964,22 +973,33 @@
+Executing test function test.multiPhylo.As.multiPhylo4 ... done successfully.
+
+
+
Executing test function test.multiPhylo4.As.multiPhylo ... done successfully.
-Executing test function test.multiPhylo.As.multiPhylo4 ... done successfully.
+Executing test function test.phylo.As.phylo4 ... done successfully.
+Executing test function test.phylo.As.phylo4d ... done successfully.
+
+
+
Executing test function test.phylo4.As.data.frame ... done successfully.
Executing test function test.phylo4.As.phylo ... Error in asMethod(object) :
(converted from warning) trees with unknown order may be unsafe in ape
-In addition: Warning message:
-In rm(ExContDataFile) : object 'ExContDataFile' not found
+In addition: Warning messages:
+1: In rm(ExContDataFile) : object 'ExContDataFile' not found
+2: In asMethod(object) : trees with unknown order may be unsafe in ape
+3: In asMethod(object) : losing data while coercing phylo4d to phylo
+4: In asMethod(object) : trees with unknown order may be unsafe in ape
done successfully.
@@ -988,6 +1008,10 @@
+Executing test function test.phylo4ToDataFrame ... done successfully.
+
+
+
Executing test function test.phylo4d.As.phylo ... Error in asMethod(object) :
(converted from warning) losing data while coercing phylo4d to phylo
In addition: Warning messages:
@@ -1002,28 +1026,13 @@
-Executing test function test.phylo4ToDataFrame ... done successfully.
-
-
-
-Executing test function test.phylo.As.phylo4 ... done successfully.
-
-
-
-Executing test function test.phylo.As.phylo4d ... done successfully.
-
-
-
Executing test function test.extractTree ... done successfully.
Executing test function test.subset.phylo4 ... Error in .local(x, ...) : 0 or 1 tips would remain after subsetting
-In addition: Warning messages:
-1: In asMethod(object) : losing data while coercing phylo4d to phylo
-2: In asMethod(object) : trees with unknown order may be unsafe in ape
-3: In asMethod(object) : losing data while coercing phylo4d to phylo
-4: In asMethod(object) : trees with unknown order may be unsafe in ape
+In addition: Warning message:
+In asMethod(object) : losing data while coercing phylo4d to phylo
Error in .local(x, ...) : 0 or 1 tips would remain after subsetting
In addition: Warning message:
In .local(x, ...) : invalid nodes ignored: t999
@@ -1059,19 +1068,19 @@
-Executing test function test.phylobubbles ... done successfully.
+Executing test function test.phyloXXYY ... done successfully.
-Executing test function test.phyloXXYY ... done successfully.
+Executing test function test.phylobubbles ... done successfully.
-Executing test function test.plotOneTree ... done successfully.
+Executing test function test.plot.phylo4 ... done successfully.
-Executing test function test.plot.phylo4 ... done successfully.
+Executing test function test.plotOneTree ... done successfully.
@@ -1095,6 +1104,10 @@
+Executing test function test.MRCA ... done successfully.
+
+
+
Executing test function test.ancestor ... done successfully.
@@ -1139,10 +1152,6 @@
-Executing test function test.MRCA ... done successfully.
-
-
-
Executing test function test.shortestPath ... done successfully.
@@ -1151,16 +1160,13 @@
------------------- UNIT TEST SUMMARY ---------------------
-RUNIT TEST PROTOCOL -- Tue Nov 23 20:27:56 2010
+RUNIT TEST PROTOCOL -- Thu Mar 24 15:56:02 2011
***********************************************
-Number of test functions: 97
+Number of test functions: 100
Number of errors: 0
Number of failures: 0
1 Test Suite :
-phylobase unit testing - 97 test functions, 0 errors, 0 failures
+phylobase unit testing - 100 test functions, 0 errors, 0 failures
>
-> proc.time()
- user system elapsed
- 11.48 0.14 11.65
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