[Phylobase-commits] r839 - pkg/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Nov 23 21:26:17 CET 2012
Author: bbolker
Date: 2012-11-23 21:26:17 +0100 (Fri, 23 Nov 2012)
New Revision: 839
Removed:
pkg/tests/doRUnit.Rout.save
Modified:
pkg/tests/roundtrip.Rout.save
Log:
REMOVE doRUnit.Rout.save (results not consistent across machines,
leading to lots of false positives)
Deleted: pkg/tests/doRUnit.Rout.save
===================================================================
--- pkg/tests/doRUnit.Rout.save 2012-11-23 20:13:30 UTC (rev 838)
+++ pkg/tests/doRUnit.Rout.save 2012-11-23 20:26:17 UTC (rev 839)
@@ -1,1175 +0,0 @@
-
-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 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.
-
-> ## 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")
-+ }
-
-Running unit tests
-$pkg
-[1] "phylobase"
-
-$getwd
-[1] "/mnt/hgfs/bolker/Documents/R/pkgs/phylobase/pkg/tests"
-
-$pathToUnitTests
-[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’
-
-The following object is masked from ‘package:ape’:
-
- edges
-
-
-
-Executing test function test.checkTree ... storing read block: TAXA
-Error in readNCL(file = file, simplify = simplify, type = type, char.all = char.all, :
- Unknown taxon D s strain in TRANSLATE command.
-The translate key 2 has NOT been added to the translation table!
- done successfully.
-
-
-
-Executing test function test.phylo4d.matrix ... done successfully.
-
-
-
-Executing test function test.phylo4d.phylo ... done successfully.
-
-
-
-Executing test function test.phylo4d.phylo4 ... Error in formatData(phy = x, dt = tip.data, type = "tip", ...) :
- The following nodes are not found in the dataset: t1, t2, t3, t4, t5
-In addition: Warning messages:
-1: In checkTree(object) : Labels are not unique
-2: In checkTree(object) : Labels are not unique
-Error in formatData(phy = x, dt = node.data, type = "internal", ...) :
- Your node data are being matched to tip nodes. Make sure that your data identifiers are correct.
- done successfully.
-
-
-
-Executing test function test.phylo4d.phylo4d ... Error in phylo4d(phyd) :
- Your object is already a phylo4d object. If you want to modify the data attached to it look at the help for tdata()<-
- done successfully.
-
-
-
-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
-Error : label.column %in% names(dt) is not TRUE
-Error in formatData(phy.alt, data.frame(a = 1:5, row.names = c(rev(lab.tip)[1:3], :
- The following nodes are not found in the dataset: t1, t2
-Error in formatData(phy.alt, data.frame(a = 1:5, lab = c(rev(lab.tip)[1:3], :
- The following nodes are not found in the dataset: t1, t2
-Error in formatData(phy.alt, data.frame(a = 1:5, row.names = 4:8), type = "tip") :
- Your tip data are being matched to internal nodes. Make sure that your data identifiers are correct.
-Error in formatData(phy.alt, data.frame(a = 6:9, row.names = 1:4), type = "internal") :
- Your node data are being matched to tip nodes. Make sure that your data identifiers are correct.
-Error in formatData(phy.alt, data.frame(a = 1:3), type = "tip") :
- The following nodes are not found in the dataset: t4, t5
-Error in formatData(phy.alt, data.frame(a = 1:3), type = "tip", missing.data = "fail") :
- The following nodes are not found in the dataset: t4, t5
-Error in formatData(phy.alt, data.frame(a = 1:3), type = "tip", missing.data = "warn") :
- (converted from warning) The following nodes are not found in the dataset: t4, t5
-Error in formatData(phy.alt, data.frame(a = 1:3), type = "tip", missing.data = "fail") :
- The following nodes are not found in the dataset: t4, t5
-Error in formatData(phy.alt, data.frame(a = 0:5, row.names = 0:5), type = "tip", :
- (converted from warning) The following names are not found in the tree: 0
-Error in formatData(phy.alt, data.frame(a = 0:5, row.names = 0:5), type = "tip") :
- (converted from warning) The following names are not found in the tree: 0
- done successfully.
-
-
-
-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
-Error in formatData(phy.dup, data.frame(a = 1:5, lab = c(rev(lab.tip)[1:3], :
- The following nodes are not found in the dataset: t1, t1
-Error in formatData(phy.dup, data.frame(a = 1:5, row.names = 4:8), type = "tip") :
- Your tip data are being matched to internal nodes. Make sure that your data identifiers are correct.
-Error in formatData(phy.dup, data.frame(a = 6:9, row.names = 1:4), type = "internal") :
- Your node data are being matched to tip nodes. Make sure that your data identifiers are correct.
-Error in formatData(phy.dup, data.frame(a = 1:3), type = "tip") :
- The following nodes are not found in the dataset: t4, t5
-Error in formatData(phy.dup, data.frame(a = 1:3), type = "tip", missing.data = "fail") :
- The following nodes are not found in the dataset: t4, t5
-Error in formatData(phy.dup, data.frame(a = 1:3), type = "tip", missing.data = "warn") :
- (converted from warning) The following nodes are not found in the dataset: t4, t5
-Error in formatData(phy.dup, data.frame(a = 1:3), type = "tip", missing.data = "fail") :
- The following nodes are not found in the dataset: t4, t5
-Error in formatData(phy.dup, data.frame(a = 0:5, row.names = 0:5), type = "tip", :
- (converted from warning) The following names are not found in the tree: 0
-Error in formatData(phy.dup, data.frame(a = 0:5, row.names = 0:5), type = "tip") :
- (converted from warning) The following names are not found in the tree: 0
- done successfully.
-
-
-
-Executing test function test.reorder.phylo ... done successfully.
-
-
-
-Executing test function test.addData.phylo4 ... done successfully.
-
-
-
-Executing test function test.addData.phylo4d ... done successfully.
-
-
-
-Executing test function test.hasNodeData.phylo4d ... done successfully.
-
-
-
-Executing test function test.na.omit.phylo4d ... done successfully.
-
-
-
-Executing test function test.nData ... 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.
-
-
-
-Executing test function test.edgeId.phylo4 ... done successfully.
-
-
-
-Executing test function test.edgeLabels.phylo4 ... done successfully.
-
-
-
-Executing test function test.edgeLength.phylo4 ... done successfully.
-
-
-
-Executing test function test.edgeOrder.phylo4 ... done successfully.
-
-
-
-Executing test function test.edges.phylo4 ... done successfully.
-
-
-
-Executing test function test.hasEdgeLabels.phylo4 ... done successfully.
-
-
-
-Executing test function test.hasEdgeLength.phylo4 ... done successfully.
-
-
-
-Executing test function test.hasNodeLabels.phylo4 ... done successfully.
-
-
-
-Executing test function test.head.phylo4 ... done successfully.
-
-
-
-Executing test function test.isRooted.phylo4 ... done successfully.
-
-
-
-Executing test function test.isUltrametric ... Error in isUltrametric(tmpPhy) : The tree has no edge lengths.
- done successfully.
-
-
-
-Executing test function test.labels.phylo4 ... done successfully.
-
-
-
-Executing test function test.names.phylo4 ... done successfully.
-
-
-
-Executing test function test.nEdges.phylo4 ... done successfully.
-
-
-
-Executing test function test.nNodes.phylo4 ... done successfully.
-
-
-
-Executing test function test.nodeDepth.phylo4 ... done successfully.
-
-
-
-Executing test function test.nodeId.phylo4 ... done successfully.
-
-
-
-Executing test function test.nodeLabels.phylo4 ... done successfully.
-
-
-
-Executing test function test.nodeType.phylo4 ... done successfully.
-
-
-
-Executing test function test.nTips.ANY ... done successfully.
-
-
-
-Executing test function test.nTips.phylo4 ... done successfully.
-
-
-
-Executing test function test.reorder.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.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.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.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.rootNode.phylo4 ... 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.rootNode.phylo4 ... done successfully.
-
-
-
-Executing test function test.sumEdgeLength.phylo4 ... done successfully.
-
-
-
-Executing test function test.summary.phylo4 ... done successfully.
-
-
-
-Executing test function test.tail.phylo4 ... done successfully.
-
-
-
-Executing test function test.tipLabels.phylo4 ... done successfully.
-
-
-
-Executing test function test.assign.pdata ... done successfully.
-
-
-
-Executing test function test.check_pdata ... done successfully.
-
-
-
-Executing test function test.extract.pdata ... done successfully.
-
-
-
-Executing test function test.pdata ... done successfully.
-
-
-
-Executing test function test.plot.pdata ... done successfully.
-
-
-
-Executing test function test..genlab ... done successfully.
-
-
-
-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’
-Error in phylobase.options(foobar = "foo") :
- Option name invalid: ‘foobar’
- done successfully.
-
-
-
-Executing test function test.prune.phylo4 ... done successfully.
-
-
-
-Executing test function test.prune.phylo4d ... done successfully.
-
-
-
-Executing test function test.readNCL ...
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 8, column (approximately) 9 (file position 217)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 8, column (approximately) 9 (file position 217)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 8, column (approximately) 9 (file position 217)
-storing implied block: TAXA
-storing read block: TREES
-Error in .local(x, ...) : Labels are not unique
-In addition: Warning messages:
-1: In FUN(X[[2L]], ...) :
- Could not use value "asdata" for check.node.labels because there are no labels associated with the tree
-2: In FUN(X[[2L]], ...) :
- Could not use value "asdata" for check.node.labels because there are no labels associated with the tree
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 8, column (approximately) 9 (file position 217)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 8, column (approximately) 9 (file position 217)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 5, column (approximately) 1 (file position 37)
-storing implied block: TAXA
-storing read block: TREES
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-Error in `levels<-.factor`(`*tmp*`, value = c("test2A", "test2B")) :
- number of levels differs
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-Error in `levels<-.factor`(`*tmp*`, value = c("test2A", "test2B")) :
- number of levels differs
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-Error in `levels<-.factor`(`*tmp*`, value = c("test2A", "test2B")) :
- number of levels differs
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-Error in `levels<-.factor`(`*tmp*`, value = c("test2A", "test2B")) :
- number of levels differs
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITE
-storing read block: BROWNIE
-Error in readNCL(file = "foo.bar") :
- "foo.bar" does not refer to a valid file.
-In addition: Warning message:
-In rm(ExContDataFile) : object 'ExContDataFile' not found
-storing read block: TAXA
-storing read block: TREES
-storing read block: CHARACTERS
-Error in readNCL(file = noStateLabels, return.labels = TRUE) :
- (converted from warning) state labels are missing for 'char1', the option return.labels is thus ignored.
-storing read block: TAXA
-storing read block: TREES
-storing read block: CHARACTERS
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 1, column (approximately) 20 (file position 19)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 1, column (approximately) 20 (file position 19)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 1, column (approximately) 20 (file position 19)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 1, column (approximately) 20 (file position 19)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 1, column (approximately) 20 (file position 19)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 1, column (approximately) 20 (file position 19)
-storing implied block: TAXA
-storing read block: TREES
- done successfully.
-
-
-
-Executing test function test.readNexus ...
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 8, column (approximately) 9 (file position 217)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 8, column (approximately) 9 (file position 217)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 8, column (approximately) 9 (file position 217)
-storing implied block: TAXA
-storing read block: TREES
-Error in .local(x, ...) : Labels are not unique
-In addition: Warning messages:
-1: In readNCL(file = noStateLabels, type = "data", return.labels = TRUE) :
- state labels are missing for 'char1', the option return.labels is thus ignored.
-2: In readNCL(file = noStateLabels, type = "data", return.labels = TRUE) :
- state labels are missing for 'char2', the option return.labels is thus ignored.
-3: In readNCL(file = noStateLabels, type = "data", return.labels = TRUE) :
- state labels are missing for 'char3', the option return.labels is thus ignored.
-4: In FUN(X[[2L]], ...) :
- Could not use value "asdata" for check.node.labels because there are no labels associated with the tree
-5: In FUN(X[[2L]], ...) :
- Could not use value "asdata" for check.node.labels because there are no labels associated with the tree
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 8, column (approximately) 9 (file position 217)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 8, column (approximately) 9 (file position 217)
-storing implied block: TAXA
-storing read block: TREES
-
-Warning:
- A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block.
-at line 5, column (approximately) 1 (file position 37)
-storing implied block: TAXA
-storing read block: TREES
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-Error in `levels<-.factor`(`*tmp*`, value = c("test2A", "test2B")) :
- number of levels differs
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-Error in `levels<-.factor`(`*tmp*`, value = c("test2A", "test2B")) :
- number of levels differs
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-Error in `levels<-.factor`(`*tmp*`, value = c("test2A", "test2B")) :
- number of levels differs
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-Error in `levels<-.factor`(`*tmp*`, value = c("test2A", "test2B")) :
- number of levels differs
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITECHARMODELS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: TREES
-storing read block: ASSUMPTIONS
-storing read block: MESQUITE
-storing read block: BROWNIE
-storing read block: TAXA
-storing read block: CHARACTERS
-storing read block: CHARACTERS
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/phylobase -r 839
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