prepare 3.1.0 release

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: corehunter
 Title: Multi-Purpose Core Subset Selection
-Version: 3.0.1.9000
-Date: 2016-10-05
+Version: 3.1.0
+Date: 2017-01-27
 Authors@R: c(person("Herman", "De Beukelaer", email = "herman.debeukelaer@gmail.com", role = c("aut", "cre")),
              person("Guy", "Davenport", email = "daveneti@gmail.com", role = "aut"),
              person("Veerle", "Fack", email = "veerle.fack@ugent.be", role = "ths"))

NEWS.md

@@ -1,8 +1,8 @@
 Core Hunter 3
 =============
 
-Version 3.0.1.9000 (dev)
-------------------------
+Version 3.1.0 (27/01/2017)
+--------------------------
 
  - More informative output when printing Core Hunter data objects.
  - It is now required to explicitly specify the format when reading genotype data. Moreover, a warning is raised in case it seems that the wrong format may have been selected, through an inspection of the data that was read.

cran-comments.md

@@ -1,14 +1,6 @@
-## Resubmission
-
-This is a resubmission. In this version I have:
-
- - Made the contents of the  'Description' field in the DESCRIPTION file more comprehensive.
- - Modified the `.onLoad` function to check the available Java version (should be >= 8). The 'SystemRequirements' field in DESCRIPTION and the README also state that Java JRE 8 or higher is required.
- - Replaced 'http://www.corehunter.org' with '<http://www.corehunter.org>' in 'Desription' field for auto-linking.
-
 ## Test environments
 
-* local OS X install, R 3.2.4
+* local OS X install, R 3.3.2
 * ubuntu 12.04 (on travis-ci), R 3.2.5, R 3.3.1 & R devel
 * win-builder (devel and release)
 

tests/testthat/testData.R

@@ -109,12 +109,12 @@ test_that("print", {
   data <- distanceData()
   expect_output(print(data), "# Precomputed distance matrix")
   expect_output(print(data), "accessions = 218")
-  expect_output(print(data), "extdata/distances.csv")
+  expect_output(print(data), "extdata[\\/]*distances.csv")
 
   data <- distanceData(size = "small")
   expect_output(print(data), "# Precomputed distance matrix")
   expect_output(print(data), "accessions = 5")
-  expect_output(print(data), "testthat/data/distances-small.txt")
+  expect_output(print(data), "testthat[\\/]*data[\\/]*distances-small.txt")
 })
 
 ########################
@@ -456,47 +456,47 @@ test_that("print", {
   expect_output(print(data), "markers = 190")
   expect_output(print(data), "alleles per marker = 2")
   expect_output(print(data), "Format = default")
-  expect_output(print(data), "extdata/genotypes.csv")
+  expect_output(print(data), "extdata[\\/]*genotypes.csv")
 
   data <- genotypeData(format = "biparental")
   expect_output(print(data), "# Genotypes")
   expect_output(print(data), "accessions = 218")
   expect_output(print(data), "markers = 190")
   expect_output(print(data), "alleles per marker = 2")
   expect_output(print(data), "Format = biparental")
-  expect_output(print(data), "extdata/genotypes-biparental.csv")
+  expect_output(print(data), "extdata[\\/]*genotypes-biparental.csv")
 
   data <- genotypeData(format = "freq")
   expect_output(print(data), "# Genotypes")
   expect_output(print(data), "accessions = 218")
   expect_output(print(data), "markers = 190")
   expect_output(print(data), "alleles per marker = 2")
   expect_output(print(data), "Format = frequency")
-  expect_output(print(data), "extdata/genotypes-frequency.csv")
+  expect_output(print(data), "extdata[\\/]*genotypes-frequency.csv")
 
   data <- genotypeData(format = "default", size = "small")
   expect_output(print(data), "# Genotypes")
   expect_output(print(data), "accessions = 5")
   expect_output(print(data), "markers = 4")
   expect_output(print(data), "alleles per marker = 2-4")
   expect_output(print(data), "Format = default")
-  expect_output(print(data), "testthat/data/genotypes-small.csv")
+  expect_output(print(data), "testthat[\\/]*data[\\/]*genotypes-small.csv")
 
   data <- genotypeData(format = "biparental", size = "small")
   expect_output(print(data), "# Genotypes")
   expect_output(print(data), "accessions = 5")
   expect_output(print(data), "markers = 4")
   expect_output(print(data), "alleles per marker = 2")
   expect_output(print(data), "Format = biparental")
-  expect_output(print(data), "testthat/data/genotypes-bi-small.csv")
+  expect_output(print(data), "testthat[\\/]*data[\\/]*genotypes-bi-small.csv")
 
   data <- genotypeData(format = "freq", size = "small")
   expect_output(print(data), "# Genotypes")
   expect_output(print(data), "accessions = 5")
   expect_output(print(data), "markers = 4")
   expect_output(print(data), "alleles per marker = 2-4")
   expect_output(print(data), "Format = frequency")
-  expect_output(print(data), "testthat/data/genotypes-freq-small.csv")
+  expect_output(print(data), "testthat[\\/]*data[\\/]*genotypes-freq-small.csv")
 })
 
 #########################
@@ -663,15 +663,15 @@ test_that("print", {
   expect_output(print(data), "traits = 4")
   expect_output(print(data), "qualitative traits = 0")
   expect_output(print(data), "quantitative traits = 4")
-  expect_output(print(data), "extdata/phenotypes.csv")
+  expect_output(print(data), "extdata[\\/]*phenotypes.csv")
 
   data <- phenotypeData(size = "small")
   expect_output(print(data), "# Phenotypes")
   expect_output(print(data), "accessions = 5")
   expect_output(print(data), "traits = 5")
   expect_output(print(data), "qualitative traits = 2")
   expect_output(print(data), "quantitative traits = 3")
-  expect_output(print(data), "testthat/data/phenotypes-small.csv")
+  expect_output(print(data), "testthat[\\/]*data[\\/]*phenotypes-small.csv")
 })
 
 ###########################