[med-svn] r21673 - in trunk/packages/R/r-cran-rnexml/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2016-04-08 11:27:07 +0000 (Fri, 08 Apr 2016)
New Revision: 21673

Added:
   trunk/packages/R/r-cran-rnexml/trunk/debian/patches/
   trunk/packages/R/r-cran-rnexml/trunk/debian/patches/exclude_geiger_from_tests.patch
   trunk/packages/R/r-cran-rnexml/trunk/debian/patches/series
Log:
Exlude tests that are requiring r-cran-geiger which is not yet packaged


Added: trunk/packages/R/r-cran-rnexml/trunk/debian/patches/exclude_geiger_from_tests.patch
===================================================================
--- trunk/packages/R/r-cran-rnexml/trunk/debian/patches/exclude_geiger_from_tests.patch	                        (rev 0)
+++ trunk/packages/R/r-cran-rnexml/trunk/debian/patches/exclude_geiger_from_tests.patch	2016-04-08 11:27:07 UTC (rev 21673)
@@ -0,0 +1,107 @@
+--- a/tests/testthat/geiger_test.R
++++ /dev/null
+@@ -1,56 +0,0 @@
+-context("Geiger tests (may take 15+ minutes)")
+-
+-
+-library(geiger)
+-
+-
+-test_that("We can write caudata data to nexml", {
+-  data(caudata)
+-  nexml_write(trees = caudata$phy, characters = caudata$dat, file="tmp.xml")
+-  expect_true_or_null(nexml_validate("tmp.xml"))
+-  unlink("tmp.xml") # cleanup
+-})
+-
+-
+-test_that("We can write geospiza data to nexml", {
+-  data(geospiza)
+-  nexml_write(trees = geospiza$phy, characters = geospiza$dat, file="tmp.xml")
+-  expect_true_or_null(nexml_validate("tmp.xml"))
+-  unlink("tmp.xml") # cleanup
+-})
+-
+-test_that("We can write chelonia data to nexml", {
+-  data(chelonia)
+-  nexml_write(trees = chelonia$phy, characters = chelonia$dat, file="tmp.xml")
+-  expect_true_or_null(nexml_validate("tmp.xml"))
+-  unlink("tmp.xml") # cleanup
+-})
+-
+-test_that("We can write primates data to nexml", {
+-  data(primates)
+-  nexml_write(trees = primates$phy, characters = primates$dat, file="tmp.xml")
+-  expect_true_or_null(nexml_validate("tmp.xml"))
+-  unlink("tmp.xml") # cleanup
+-})
+-
+-test_that("We can write whales data to nexml", {
+-  data(whales)
+-# taxa need to be rownames not separate column 
+-  whales$dat <- whales$richness[[2]]
+-  names(whales$dat) <- whales$richness[[1]] 
+-  nexml_write(trees = whales$phy, characters = whales$dat, file="tmp.xml")
+-  expect_true_or_null(nexml_validate("tmp.xml"))
+-  unlink("tmp.xml") # cleanup
+-})
+-
+-
+-test_that("We can write amphibia multiphylo to nexml. Two of these phylogenies each have nearly 3K taxa, so this may take around 12 minutes", {
+-# multiphylo, where two phylogenies have each nearly 3K taxa
+-  data(amphibia)
+-  class(amphibia) <- "multiPhylo"
+-  runtime <- system.time(nexml_write(amphibia, file="tmp.xml")) # Slow! about 12 minutes
+-
+-  expect_true_or_null(nexml_validate("tmp.xml"))
+-  unlink("tmp.xml") # cleanup
+-})
+-
+--- a/tests/testthat/test_comp_analysis.R
++++ /dev/null
+@@ -1,29 +0,0 @@
+-context("Comparative analysis")
+-
+-
+-library(geiger)
+-
+-
+-test_that("We can extract tree and trait data to run fitContinuous and fitDiscrete", {
+-  nexml <- read.nexml(system.file("examples", "comp_analysis.xml", package="RNeXML"))
+-  traits <- get_characters(nexml)
+-  tree <- get_trees(nexml)
+-  expect_is(tree, "phylo")
+-  cts <- fitContinuous(tree, traits[1], ncores=1)
+-  ## Incredibly, fitDiscrete cannot take discrete characters
+-  # dte <- fitDiscrete(tree, traits[2], ncores=1)
+-  traits[[2]] <- as.numeric(traits[[2]])
+-  dte <- fitDiscrete(tree, traits[2], ncores=1)
+-  
+-})
+-
+-
+-test_that("We can serialize tree and trait data for a comparative analysis", {
+-  data(geospiza)
+-  add_trees(geospiza$phy)
+-  nexml <- add_characters(geospiza$dat)
+-  write.nexml(nexml, file = "geospiza.xml")
+-  expect_true_or_null(nexml_validate("geospiza.xml"))
+-  unlink("geospiza.xml")
+-})
+-
+--- a/tests/testthat/test_characters.R
++++ b/tests/testthat/test_characters.R
+@@ -101,13 +101,3 @@ test_that("we can add characters to a ne
+ 
+ 
+ 
+-## based on bug on 2014-03-12 65ae459523c529452adb699c3d5d118c0a207402 
+-test_that("we can add multiple character matrices to a nexml file", {
+-          library("geiger")
+-          data(geospiza)
+-          data(primates)
+-          nex <- add_characters(geospiza$dat)
+-          nex <- add_characters(primates$dat, nex)
+-          expect_is(nex, "nexml")
+-})
+-

Added: trunk/packages/R/r-cran-rnexml/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-cran-rnexml/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/R/r-cran-rnexml/trunk/debian/patches/series	2016-04-08 11:27:07 UTC (rev 21673)
@@ -0,0 +1 @@
+exclude_geiger_from_tests.patch