[Phylobase-commits] r837 - in pkg: src tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 21 23:45:34 CET 2012
Author: bbolker
Date: 2012-11-21 23:45:34 +0100 (Wed, 21 Nov 2012)
New Revision: 837
Modified:
pkg/src/nxstreesblock.cpp
pkg/tests/doRUnit.Rout.save
Log:
make nexus reading a lot quieter
update test output
Modified: pkg/src/nxstreesblock.cpp
===================================================================
--- pkg/src/nxstreesblock.cpp 2012-11-21 22:12:12 UTC (rev 836)
+++ pkg/src/nxstreesblock.cpp 2012-11-21 22:45:34 UTC (rev 837)
@@ -1330,9 +1330,9 @@
else if (prevToken == NXS_TREE_COLON_TOKEN)
throw NxsException("Expecting a branch length after a : but found (", token);
nchildren.top() += 1;
- Rcpp::Rcerr << "Open Parens nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ // Rcpp::Rcerr << "Open Parens nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
nchildren.push(0);
- Rcpp::Rcerr << "Open Parens after push nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ // Rcpp::Rcerr << "Open Parens after push nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
newickStream << '(';
prevToken = NXS_TREE_OPEN_PARENS_TOKEN;
handled = true;
@@ -1356,10 +1356,10 @@
else if (nchildren.top() > 3 || nchildren.size() > 1) /* three children are allowed not considered a polytomy */
hasPolytomies = true;
}
- Rcpp::Rcerr << "close parens nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ // Rcpp::Rcerr << "close parens nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
nchildren.pop();
- if (!nchildren.empty())
- Rcpp::Rcerr << "close parens post-pop nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ // if (!nchildren.empty())
+ // Rcpp::Rcerr << "close parens post-pop nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
newickStream << ')';
prevToken = NXS_TREE_CLOSE_PARENS_TOKEN;
handled = true;
@@ -1433,7 +1433,7 @@
NxsString toAppend;
if (prevToken == NXS_TREE_CLOSE_PARENS_TOKEN)
{
- Rcpp::Rcerr << "validateInternalNodeLabels = " << validateInternalNodeLabels << '\n';
+ // Rcpp::Rcerr << "validateInternalNodeLabels = " << validateInternalNodeLabels << '\n';
if (validateInternalNodeLabels)
{
std::map<std::string, unsigned>::const_iterator tt = capNameToInd.find(ucl);
@@ -1517,7 +1517,7 @@
}
taxaEncountered.insert(indWithAdditions);
nchildren.top() += 1;
- Rcpp::Rcerr << "treating as number " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ // Rcpp::Rcerr << "treating as number " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
toAppend += (1 + indWithAdditions);
}
@@ -1543,7 +1543,7 @@
capNameToInd[tasstring] = valueInd;
taxaEncountered.insert(valueInd);
nchildren.top() += 1;
- Rcpp::Rcerr << "nonnumeric newtaxon " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ // Rcpp::Rcerr << "nonnumeric newtaxon " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
toAppend += (1 + valueInd);
}
}
@@ -1559,7 +1559,7 @@
}
taxaEncountered.insert(*cit);
nchildren.top() += 1;
- Rcpp::Rcerr << "taxon set " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ // Rcpp::Rcerr << "taxon set " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
if (!firstTaxonAdded)
toAppend.append(1, ',');
toAppend += (1 + *cit);
@@ -1576,7 +1576,7 @@
{
taxaEncountered.insert(ind);
nchildren.top() += 1;
- Rcpp::Rcerr << "taxon label " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ // Rcpp::Rcerr << "taxon label " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
toAppend += (1 + ind);
}
}
Modified: pkg/tests/doRUnit.Rout.save
===================================================================
--- pkg/tests/doRUnit.Rout.save 2012-11-21 22:12:12 UTC (rev 836)
+++ pkg/tests/doRUnit.Rout.save 2012-11-21 22:45:34 UTC (rev 837)
@@ -1,13 +1,15 @@
-R version 2.12.2 (2011-02-25)
-Copyright (C) 2011 The R Foundation for Statistical Computing
+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: x86_64-pc-linux-gnu (64-bit)
+Platform: i686-pc-linux-gnu (32-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.
@@ -84,18 +86,18 @@
[1] "phylobase"
$getwd
-[1] "/home/francois/R-dev/phylobase/pkg.Rcheck/tests"
+[1] "/mnt/hgfs/bolker/Documents/R/pkgs/phylobase/pkg/tests"
$pathToUnitTests
-[1] "/home/francois/R-dev/phylobase/pkg.Rcheck/phylobase/unitTests"
+[1] "/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/phylobase/unitTests"
Loading required package: grid
Loading required package: ape
Loading required package: Rcpp
-Attaching package: 'phylobase'
+Attaching package: ‘phylobase’
-The following object(s) are masked from 'package:ape':
+The following object is masked from ‘package:ape’:
edges
@@ -109,24 +111,6 @@
-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.phylo4d.matrix ... done successfully.
@@ -152,6 +136,24 @@
+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.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
@@ -210,59 +212,54 @@
-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.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.addData.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.hasNodeData.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.na.omit.phylo4d ... done successfully.
-Executing test function test.Replace.rootNode.phylo4 ... done successfully.
+Executing test function test.nData ... 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.nodeData.phylo4d ... done successfully.
+Executing test function test.Replace.nodeData.phylo4d ... done successfully.
+
+
+
+Executing test function test.Replace.tdata.phylo4d ... done successfully.
+
+
+
+Executing test function test.Replace.tipData.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.depthTips.phylo4 ... done successfully.
@@ -316,26 +313,18 @@
-Executing test function test.nEdges.phylo4 ... done successfully.
+Executing test function test.names.phylo4 ... done successfully.
-Executing test function test.nNodes.phylo4 ... done successfully.
+Executing test function test.nEdges.phylo4 ... done successfully.
-Executing test function test.nTips.ANY ... done successfully.
+Executing test function test.nNodes.phylo4 ... done successfully.
-Executing test function test.nTips.phylo4 ... done successfully.
-
-
-
-Executing test function test.names.phylo4 ... done successfully.
-
-
-
Executing test function test.nodeDepth.phylo4 ... done successfully.
@@ -352,78 +341,91 @@
-Executing test function test.reorder.phylo4 ... done successfully.
+Executing test function test.nTips.ANY ... done successfully.
-Executing test function test.rootNode.phylo4 ... done successfully.
+Executing test function test.nTips.phylo4 ... done successfully.
-Executing test function test.sumEdgeLength.phylo4 ... done successfully.
+Executing test function test.reorder.phylo4 ... done successfully.
-Executing test function test.summary.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.tail.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.tipLabels.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.Replace.nodeData.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.Replace.tdata.phylo4d ... done successfully.
+Executing test function test.Replace.rootNode.phylo4 ... done successfully.
-Executing test function test.Replace.tipData.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.addData.phylo4 ... done successfully.
+Executing test function test.rootNode.phylo4 ... done successfully.
-Executing test function test.addData.phylo4d ... done successfully.
+Executing test function test.sumEdgeLength.phylo4 ... done successfully.
-Executing test function test.hasNodeData.phylo4d ... done successfully.
+Executing test function test.summary.phylo4 ... done successfully.
-Executing test function test.nData ... done successfully.
+Executing test function test.tail.phylo4 ... done successfully.
-Executing test function test.na.omit.phylo4d ... done successfully.
+Executing test function test.tipLabels.phylo4 ... 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.
@@ -449,10 +451,10 @@
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.
@@ -973,33 +975,22 @@
-Executing test function test.multiPhylo.As.multiPhylo4 ... done successfully.
-
-
-
Executing test function test.multiPhylo4.As.multiPhylo ... done successfully.
-Executing test function test.phylo.As.phylo4 ... done successfully.
+Executing test function test.multiPhylo.As.multiPhylo4 ... 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 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
+In addition: Warning message:
+In rm(ExContDataFile) : object 'ExContDataFile' not found
done successfully.
@@ -1008,16 +999,11 @@
-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:
1: In asMethod(object) : trees with unknown order may be unsafe in ape
2: In asMethod(object) : losing data while coercing phylo4d to phylo
-3: In asMethod(object) : trees with unknown order may be unsafe in ape
Error in asMethod(object) :
(converted from warning) losing data while coercing phylo4d to phylo
In addition: Warning message:
@@ -1026,13 +1012,26 @@
+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 message:
-In asMethod(object) : losing data while coercing phylo4d to phylo
+In addition: Warning messages:
+1: In asMethod(object) : losing data while coercing phylo4d to phylo
+2: 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
@@ -1040,7 +1039,8 @@
In addition: Warning message:
In .local(x, ...) : invalid nodes ignored: t999
Error in subset(phyd, tips.include = "t1", tips.exclude = "t3") :
- error in evaluating the argument 'x' in selecting a method for function 'subset'
+ error in evaluating the argument 'x' in selecting a method for function 'subset': Error: object 'phyd' not found
+
done successfully.
@@ -1068,19 +1068,19 @@
-Executing test function test.phyloXXYY ... done successfully.
+Executing test function test.phylobubbles ... done successfully.
-Executing test function test.phylobubbles ... done successfully.
+Executing test function test.phyloXXYY ... done successfully.
-Executing test function test.plot.phylo4 ... done successfully.
+Executing test function test.plotOneTree ... done successfully.
-Executing test function test.plotOneTree ... done successfully.
+Executing test function test.plot.phylo4 ... done successfully.
@@ -1104,10 +1104,6 @@
-Executing test function test.MRCA ... done successfully.
-
-
-
Executing test function test.ancestor ... done successfully.
@@ -1152,6 +1148,10 @@
+Executing test function test.MRCA ... done successfully.
+
+
+
Executing test function test.shortestPath ... done successfully.
@@ -1160,7 +1160,7 @@
------------------- UNIT TEST SUMMARY ---------------------
-RUNIT TEST PROTOCOL -- Thu Mar 24 15:56:02 2011
+RUNIT TEST PROTOCOL -- Wed Nov 21 17:43:24 2012
***********************************************
Number of test functions: 100
Number of errors: 0
@@ -1170,3 +1170,6 @@
1 Test Suite :
phylobase unit testing - 100 test functions, 0 errors, 0 failures
>
+> proc.time()
+ user system elapsed
+ 8.500 3.376 11.868
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