[Phylobase-commits] r838 - pkg/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Nov 23 21:13:31 CET 2012
Author: bbolker
Date: 2012-11-23 21:13:30 +0100 (Fri, 23 Nov 2012)
New Revision: 838
Added:
pkg/tests/RUnit-tests.R
pkg/tests/RUnit-tests.Rout.save
pkg/tests/dUnit.Rout.save
pkg/tests/roundtripUnit-tests.Rout.save
Modified:
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/testprune.Rout.save
Log:
new versions of .Rout.save
Added: pkg/tests/RUnit-tests.R
===================================================================
--- pkg/tests/RUnit-tests.R (rev 0)
+++ pkg/tests/RUnit-tests.R 2012-11-23 20:13:30 UTC (rev 838)
@@ -0,0 +1,7 @@
+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)
Added: pkg/tests/RUnit-tests.Rout.save
===================================================================
--- pkg/tests/RUnit-tests.Rout.save (rev 0)
+++ pkg/tests/RUnit-tests.Rout.save 2012-11-23 20:13:30 UTC (rev 838)
@@ -0,0 +1,32 @@
+
+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
Added: pkg/tests/dUnit.Rout.save
===================================================================
--- pkg/tests/dUnit.Rout.save (rev 0)
+++ pkg/tests/dUnit.Rout.save 2012-11-23 20:13:30 UTC (rev 838)
@@ -0,0 +1 @@
+Fatal error: cannot open file 'dUnit.R': No such file or directory
Modified: pkg/tests/misctests.Rout.save
===================================================================
--- pkg/tests/misctests.Rout.save 2012-11-21 22:45:34 UTC (rev 837)
+++ pkg/tests/misctests.Rout.save 2012-11-23 20:13:30 UTC (rev 838)
@@ -1,8 +1,8 @@
-R version 2.12.0 (2010-10-15)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R Under development (unstable) (2012-11-20 r61133) -- "Unsuffered Consequences"
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: 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.
@@ -23,9 +23,9 @@
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
@@ -155,7 +155,7 @@
Mean :3 Mean :NaN
3rd Qu.:4 3rd Qu.: NA
Max. :5 Max. : NA
- NA's : 5
+ NA's :5
Nodes: data.frame with 4 internal nodes and 2 variables
@@ -166,7 +166,7 @@
Mean :NaN Mean :7.50
3rd Qu.: NA 3rd Qu.:8.25
Max. : NA Max. :9.00
- NA's : 4
+ NA's :4
>
> plot(p1)
>
@@ -497,4 +497,4 @@
>
> proc.time()
user system elapsed
- 2.980 0.020 2.999
+ 3.260 2.556 5.671
Modified: pkg/tests/nexusdata.Rout.save
===================================================================
--- pkg/tests/nexusdata.Rout.save 2012-11-21 22:45:34 UTC (rev 837)
+++ pkg/tests/nexusdata.Rout.save 2012-11-23 20:13:30 UTC (rev 838)
@@ -1,8 +1,8 @@
-R version 2.12.0 (2010-10-15)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R Under development (unstable) (2012-11-20 r61133) -- "Unsuffered Consequences"
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: 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.
@@ -38,4 +38,4 @@
>
> proc.time()
user system elapsed
- 0.28 0.03 0.30
+ 0.304 0.372 0.519
Modified: pkg/tests/phylo4dtests.Rout.save
===================================================================
--- pkg/tests/phylo4dtests.Rout.save 2012-11-21 22:45:34 UTC (rev 837)
+++ pkg/tests/phylo4dtests.Rout.save 2012-11-23 20:13:30 UTC (rev 838)
@@ -1,8 +1,8 @@
-R version 2.12.0 (2010-10-15)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R Under development (unstable) (2012-11-20 r61133) -- "Unsuffered Consequences"
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: 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.
@@ -23,9 +23,9 @@
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
@@ -92,4 +92,4 @@
>
> proc.time()
user system elapsed
- 1.390 0.030 1.423
+ 1.908 2.216 3.978
Modified: pkg/tests/phylosubtest.Rout.save
===================================================================
--- pkg/tests/phylosubtest.Rout.save 2012-11-21 22:45:34 UTC (rev 837)
+++ pkg/tests/phylosubtest.Rout.save 2012-11-23 20:13:30 UTC (rev 838)
@@ -1,8 +1,8 @@
-R version 2.12.0 (2010-10-15)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R Under development (unstable) (2012-11-20 r61133) -- "Unsuffered Consequences"
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: 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.
@@ -24,9 +24,9 @@
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
@@ -47,4 +47,4 @@
>
> proc.time()
user system elapsed
- 1.010 0.050 1.065
+ 1.704 2.288 3.855
Modified: pkg/tests/phylotorture.Rout.save
===================================================================
--- pkg/tests/phylotorture.Rout.save 2012-11-21 22:45:34 UTC (rev 837)
+++ pkg/tests/phylotorture.Rout.save 2012-11-23 20:13:30 UTC (rev 838)
@@ -1,8 +1,8 @@
-R version 2.12.0 (2010-10-15)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R Under development (unstable) (2012-11-20 r61133) -- "Unsuffered Consequences"
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: 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.
@@ -25,9 +25,9 @@
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
@@ -130,11 +130,15 @@
[1] "Error in .createLabels(value = tip.label, ntips = ntips, nnodes = nnodes, : \n Number of labels does not match number of nodes.\n"
attr(,"class")
[1] "try-error"
+attr(,"condition")
+<simpleError in .createLabels(value = tip.label, ntips = ntips, nnodes = nnodes, type = "tip"): Number of labels does not match number of nodes.>
> ## error regarding number of tip labels vs edges and nodes
> print(try(phylo4(broke2$edge), silent=TRUE))
[1] "Error in .local(x, ...) : \n tips and nodes incorrectly numbered, One or more tip/node label has an unmatched ID name Use tipLabels<- (and nodeLabels<- if needed) to update them.\n"
attr(,"class")
[1] "try-error"
+attr(,"condition")
+<simpleError in .local(x, ...): tips and nodes incorrectly numbered, One or more tip/node label has an unmatched ID name Use tipLabels<- (and nodeLabels<- if needed) to update them.>
Warning message:
In tips == 1:ntips :
longer object length is not a multiple of shorter object length
@@ -175,10 +179,14 @@
[1] "Error in .local(x, ...) : \n tips and nodes incorrectly numbered, All tips must have associated tip labels. Use tipLabels<- (and nodeLabels<- if needed) to update them., One or more tip/node label has an unmatched ID name Use tipLabels<- (and nodeLabels<- if needed) to update them.\n"
attr(,"class")
[1] "try-error"
+attr(,"condition")
+<simpleError in .local(x, ...): tips and nodes incorrectly numbered, All tips must have associated tip labels. Use tipLabels<- (and nodeLabels<- if needed) to update them., One or more tip/node label has an unmatched ID name Use tipLabels<- (and nodeLabels<- if needed) to update them.>
> print(try(phylo4(broke4$edge),silent=TRUE)) # error message saying tree has more than one root
[1] "Error in .local(x, ...) : \n tips and nodes incorrectly numbered, All tips must have associated tip labels. Use tipLabels<- (and nodeLabels<- if needed) to update them., One or more tip/node label has an unmatched ID name Use tipLabels<- (and nodeLabels<- if needed) to update them.\n"
attr(,"class")
[1] "try-error"
+attr(,"condition")
+<simpleError in .local(x, ...): tips and nodes incorrectly numbered, All tips must have associated tip labels. Use tipLabels<- (and nodeLabels<- if needed) to update them., One or more tip/node label has an unmatched ID name Use tipLabels<- (and nodeLabels<- if needed) to update them.>
> # print(try(plot(broke4), TRUE)) ## CAUSES R TO HANG!
>
> ###
@@ -190,6 +198,8 @@
[1] "Error in treePlot(x, ...) : treePlot function requires a rooted tree.\n"
attr(,"class")
[1] "try-error"
+attr(,"condition")
+<simpleError in treePlot(x, ...): treePlot function requires a rooted tree.>
>
> foo at label <- c(rep('blah',10), rep("",9))
>
@@ -203,4 +213,4 @@
>
> proc.time()
user system elapsed
- 1.130 0.010 1.148
+ 1.876 2.224 3.954
Modified: pkg/tests/plottest.Rout.save
===================================================================
--- pkg/tests/plottest.Rout.save 2012-11-21 22:45:34 UTC (rev 837)
+++ pkg/tests/plottest.Rout.save 2012-11-23 20:13:30 UTC (rev 838)
@@ -1,8 +1,8 @@
-R version 2.12.0 (2010-10-15)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R Under development (unstable) (2012-11-20 r61133) -- "Unsuffered Consequences"
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: 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.
@@ -23,9 +23,9 @@
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
@@ -46,14 +46,6 @@
>
>
> g2B <- as(extractTree(g2), "phylog")
-Loading required package: ade4
-
-Attaching package: 'ade4'
-
-The following object(s) are masked from 'package:base':
-
- within
-
Warning messages:
1: In asMethod(object) : trees with unknown order may be unsafe in ape
2: In asMethod(object) :
@@ -88,18 +80,19 @@
+ ## text(cmdpos[,1],cmdpos[,2],abbreviate(rownames(mdspos)))
+ }
Loading required package: MASS
-initial value 12.762561
-iter 5 value 1.542275
-iter 10 value 0.973859
-iter 15 value 0.657199
-iter 20 value 0.567848
-iter 25 value 0.347518
-iter 30 value 0.132855
-iter 35 value 0.047279
-iter 40 value 0.033890
-iter 45 value 0.018117
-final value 0.006328
-converged
+initial value 12.162947
+iter 5 value 3.201793
+iter 10 value 1.433796
+iter 15 value 1.147120
+iter 20 value 0.914894
+iter 25 value 0.705057
+iter 30 value 0.376895
+iter 35 value 0.256479
+iter 40 value 0.091883
+iter 45 value 0.024262
+iter 50 value 0.010918
+final value 0.010918
+stopped after 50 iterations
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
@@ -113,4 +106,4 @@
>
> proc.time()
user system elapsed
- 1.72 0.03 1.75
+ 2.352 2.468 4.674
Added: pkg/tests/roundtripUnit-tests.Rout.save
===================================================================
--- pkg/tests/roundtripUnit-tests.Rout.save (rev 0)
+++ pkg/tests/roundtripUnit-tests.Rout.save 2012-11-23 20:13:30 UTC (rev 838)
@@ -0,0 +1 @@
+Fatal error: cannot open file 'roundtripUnit-tests.R': No such file or directory
Modified: pkg/tests/testprune.Rout.save
===================================================================
--- pkg/tests/testprune.Rout.save 2012-11-21 22:45:34 UTC (rev 837)
+++ pkg/tests/testprune.Rout.save 2012-11-23 20:13:30 UTC (rev 838)
@@ -1,8 +1,8 @@
-R version 2.12.0 (2010-10-15)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R Under development (unstable) (2012-11-20 r61133) -- "Unsuffered Consequences"
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: 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.
@@ -23,9 +23,9 @@
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
@@ -86,4 +86,4 @@
>
> proc.time()
user system elapsed
- 1.330 0.030 1.362
+ 1.852 2.220 3.939
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