[Phylobase-commits] r822 - pkg/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 24 02:33:28 CET 2010
Author: francois
Date: 2010-11-24 02:33:22 +0100 (Wed, 24 Nov 2010)
New Revision: 822
Modified:
pkg/tests/RUnit-tests.Rout.save
pkg/tests/doRUnit.Rout.save
pkg/tests/misctests.Rout.save
pkg/tests/nexusdata.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.Rout.save
pkg/tests/testprune.Rout.save
Log:
update output for tests
Modified: pkg/tests/RUnit-tests.Rout.save
===================================================================
--- pkg/tests/RUnit-tests.Rout.save 2010-11-23 20:05:07 UTC (rev 821)
+++ pkg/tests/RUnit-tests.Rout.save 2010-11-24 01:33:22 UTC (rev 822)
@@ -1,7 +1,8 @@
-R version 2.10.1 (2009-12-14)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+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.
@@ -28,4 +29,4 @@
>
> proc.time()
user system elapsed
- 0.376 0.028 0.399
+ 0.34 0.02 0.36
Modified: pkg/tests/doRUnit.Rout.save
===================================================================
--- pkg/tests/doRUnit.Rout.save 2010-11-23 20:05:07 UTC (rev 821)
+++ pkg/tests/doRUnit.Rout.save 2010-11-24 01:33:22 UTC (rev 822)
@@ -1,7 +1,8 @@
-R version 2.10.1 (2009-12-14)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+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.
@@ -85,7 +86,7 @@
[1] "phylobase"
$getwd
-[1] "/home/francois/Work/R-dev/phylobase/pkg/tests"
+[1] "/home/francois/R-dev/phylobase/pkg/tests"
$pathToUnitTests
[1] "/home/francois/.R/library/phylobase/unitTests"
@@ -96,13 +97,20 @@
Attaching package: 'phylobase'
+The following object(s) are masked from 'package:ape':
- The following object(s) are masked from package:ape :
+ edges
- 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.
@@ -111,7 +119,7 @@
-Executing test function test.phylo4d.phylo4 ... Error in switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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
@@ -150,82 +158,58 @@
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 switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(extra.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(extra.data, warn = warning(msg), fail = stop(msg)) :
+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 ... [1] 10
-<environment: 0x935e7c4>
+<environment: 0x20e0660>
Error in formatData(phy.dup, phy.dup) :
phy.dup must be a vector, factor, matrix, or data frame
-Error in switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(extra.data, warn = warning(msg), fail = stop(msg)) :
+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 switch(extra.data, warn = warning(msg), fail = stop(msg)) :
+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.labelsAllPhylo4 ... done successfully.
-
-
-
-Executing test function test.labelsAllPhylo4d ... done successfully.
-
-
-
-Executing test function test.labelsNodePhylo4 ... done successfully.
-
-
-
-Executing test function test.labelsNodePhylo4d ... done successfully.
-
-
-
-Executing test function test.labelsTipsPhylo4 ... done successfully.
-
-
-
-Executing test function test.labelsTipsPhylo4d ... done successfully.
-
-
-
Executing test function test.reorder.phylo ... done successfully.
@@ -457,8 +441,7 @@
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 switch(mode(arg), list = temp <- arg, character = return(.phylobase.Options[arg]), :
- invalid argument: ‘1’
+Error in phylobase.options(1) : invalid argument: ‘1’
Error in phylobase.options(foobar = "foo") :
Option name invalid: ‘foobar’
done successfully.
@@ -473,22 +456,514 @@
-Executing test function test.readNexus ... Error in .local(x, ...) : Labels are not unique
+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 readNexus(file = co1File, check.node.labels = "asdata") :
- Could not use value "asdata" for check.node.labels because there are no labels associated with the tree 2
-Error in readNexus(file = treePolyDt, type = "all", levels.uniform = FALSE, :
- At this stage, it's not possible to use the combination: return.labels=TRUE for datasets that contain polymorphic characters.
-Error in readNexus(file = treePolyDt, type = "all", char.all = TRUE, levels.uniform = TRUE, :
- At this stage, it's not possible to use the combination: return.labels=TRUE for datasets that contain polymorphic characters.
-Error in readNexus(file = treePolyDt, type = "all", levels.uniform = FALSE, :
- At this stage, it's not possible to use the combination: return.labels=TRUE for datasets that contain polymorphic characters.
-Error in readNexus(file = treePolyDt, type = "all", char.all = FALSE, :
- At this stage, it's not possible to use the combination: return.labels=TRUE for datasets that contain polymorphic characters.
+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
+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
+ done successfully.
+
+
+
Executing test function test.multiPhylo4.As.multiPhylo ... done successfully.
@@ -555,7 +1030,6 @@
Error in .local(x, ...) : 0 or 1 tips would remain after subsetting
In addition: Warning message:
In .local(x, ...) : invalid nodes ignored: t999
-Error: no function to return from, jumping to top level
Error in subset(phyd, tips.include = "t1", tips.exclude = "t3") :
error in evaluating the argument 'x' in selecting a method for function 'subset'
done successfully.
@@ -677,16 +1151,16 @@
------------------- UNIT TEST SUMMARY ---------------------
-RUNIT TEST PROTOCOL -- Thu Apr 1 16:01:34 2010
+RUNIT TEST PROTOCOL -- Tue Nov 23 20:27:56 2010
***********************************************
-Number of test functions: 101
+Number of test functions: 97
Number of errors: 0
Number of failures: 0
1 Test Suite :
-phylobase unit testing - 101 test functions, 0 errors, 0 failures
+phylobase unit testing - 97 test functions, 0 errors, 0 failures
>
> proc.time()
user system elapsed
- 11.060 0.216 11.483
+ 11.48 0.14 11.65
Modified: pkg/tests/misctests.Rout.save
===================================================================
--- pkg/tests/misctests.Rout.save 2010-11-23 20:05:07 UTC (rev 821)
+++ pkg/tests/misctests.Rout.save 2010-11-24 01:33:22 UTC (rev 822)
@@ -1,7 +1,8 @@
-R version 2.10.1 (2009-12-14)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+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.
@@ -24,11 +25,10 @@
Attaching package: 'phylobase'
+The following object(s) are masked from 'package:ape':
- The following object(s) are masked from package:ape :
+ edges
- edges
-
> library(ape)
>
> set.seed(1)
@@ -121,7 +121,7 @@
> tipdat2 <- tipdat
> row.names(tipdat2)[1] <- "s1"
> t1 <- try(q1 <- phylo4d(r1,tip.data=tipdat2))
-Error in switch(missing.data, warn = warning(msg), fail = stop(msg)) :
+Error in formatData(phy = x, dt = tip.data, type = "tip", ...) :
The following nodes are not found in the dataset: t4
>
> plot(q2)
@@ -463,7 +463,7 @@
phyl4d> p4d.all2 <- phylo4d(p4, all.data = rbind(dat, nod.dat, match.data=FALSE))
Warning message:
-In switch(extra.data, warn = warning(msg), fail = stop(msg)) :
+In formatData(phy = x, dt = all.data, type = "all", ...) :
The following names are not found in the tree: match.data
> obj1 <- obj2 <- obj3 <- phylo4d(z, data.frame(wing=1:4,color=factor(c("b","w","b","b")), tail=runif(4)*10), match.data=FALSE)
>
@@ -497,4 +497,4 @@
>
> proc.time()
user system elapsed
- 3.436 0.080 3.882
+ 2.980 0.020 2.999
Modified: pkg/tests/nexusdata.Rout.save
===================================================================
--- pkg/tests/nexusdata.Rout.save 2010-11-23 20:05:07 UTC (rev 821)
+++ pkg/tests/nexusdata.Rout.save 2010-11-24 01:33:22 UTC (rev 822)
@@ -1,7 +1,8 @@
-R version 2.10.1 (2009-12-14)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+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.
@@ -37,4 +38,4 @@
>
> proc.time()
user system elapsed
- 0.280 0.036 0.304
+ 0.28 0.03 0.30
Modified: pkg/tests/phylo4dtests.Rout.save
===================================================================
--- pkg/tests/phylo4dtests.Rout.save 2010-11-23 20:05:07 UTC (rev 821)
+++ pkg/tests/phylo4dtests.Rout.save 2010-11-24 01:33:22 UTC (rev 822)
@@ -1,7 +1,8 @@
-R version 2.10.1 (2009-12-14)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+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.
@@ -24,11 +25,10 @@
Attaching package: 'phylobase'
+The following object(s) are masked from 'package:ape':
- The following object(s) are masked from package:ape :
+ edges
- 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 +92,4 @@
>
> proc.time()
user system elapsed
- 1.496 0.052 1.540
+ 1.390 0.030 1.423
Modified: pkg/tests/phylosubtest.Rout.save
===================================================================
--- pkg/tests/phylosubtest.Rout.save 2010-11-23 20:05:07 UTC (rev 821)
+++ pkg/tests/phylosubtest.Rout.save 2010-11-24 01:33:22 UTC (rev 822)
@@ -1,7 +1,8 @@
-R version 2.10.1 (2009-12-14)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+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.
@@ -25,11 +26,10 @@
Attaching package: 'phylobase'
+The following object(s) are masked from 'package:ape':
- The following object(s) are masked from package:ape :
+ edges
- edges
-
> data(geospiza)
>
> gtree <- extractTree(geospiza)
@@ -47,4 +47,4 @@
>
> proc.time()
user system elapsed
- 1.312 0.040 1.349
+ 1.010 0.050 1.065
Modified: pkg/tests/phylotorture.Rout.save
===================================================================
--- pkg/tests/phylotorture.Rout.save 2010-11-23 20:05:07 UTC (rev 821)
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/phylobase -r 822
More information about the Phylobase-commits
mailing list