@@ -1,8 +1,8 @@

 Package: OncoSimulR

 Type: Package

 Title: Forward Genetic Simulation of Cancer Progresion with Epistasis 

-Version: 2.3.3

-Date: 2016-06-23

+Version: 2.3.4

+Date: 2016-06-24

 Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),

 		     email = "rdiaz02@gmail.com"),

 	      person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"))

@@ -1,11 +1,14 @@

+Changes in version 2.3.4 (2016-06-24):

+	- Failing some tests in Win 32-bits

+	

 Changes in version 2.3.3 (2016-06-23):

 	- Vignette improvements and typo fixes.

 	- rfitness

-	- plot of fitness landscapes

-	- specify fitness by giving genotype-> fitness mapping

-	- tests showing same gene in epist./DAG/order

-	- clarified internal C++ unique/sorted in genotypes

-	- checks initMutant correct and bug initMutant mutable pos

+	- Plot of fitness landscapes

+	- Specify fitness by giving genotype-> fitness mapping

+	- Tests showing same gene in epist./DAG/order

+	- Clarified internal C++ unique/sorted in genotypes

+	- Checks initMutant correct and bug initMutant mutable pos

 	- samplePop: sample at arbitrary sizes.

 	- plot.oncosimulpop using auto for color.

 	- Mutator phenotype and gene-specific mutation rates.

@@ -159,9 +159,9 @@ test_that("eval fitness and mut OK", {

                      c(1.1, 1))

     expect_identical(evalGenotypeFitAndMut("b, e", fe, fm),

                      c(1.1, 1))

-    expect_identical(evalGenotypeFitAndMut("a, b, e", fe, fm),

+    expect_equal(evalGenotypeFitAndMut("a, b, e", fe, fm),

                      c(1.3 * 1.1, 10))

-    expect_identical(evalGenotypeFitAndMut("a, b, c, e", fe, fm),

+    expect_equal(evalGenotypeFitAndMut("a, b, c, e", fe, fm),

                      c(1.3 * 1.5 * 1.1, 10 * 5))

 })

@@ -325,37 +325,37 @@ test_that("evaluating genotype and mutator", {

     fm <- allMutatorEffects(noIntGenes = c("a" = 10,

                                            "c" = 5))

     ou <- evalAllGenotypesFitAndMut(fe, fm, order = FALSE)

-    expect_true(all(dplyr::filter(ou, Genotype == "a")[, c(2, 3)] ==

-                    c(1, 10)))

-    expect_true(all(dplyr::filter(ou, Genotype == "b")[, c(2, 3)] ==

-                    c(1, 1)))

-    expect_true(all(dplyr::filter(ou, Genotype == "c")[, c(2, 3)] ==

-                    c(1, 5)))

-    expect_true(all(dplyr::filter(ou, Genotype == "e")[, c(2, 3)] ==

-                    c(1.1, 1)))

-    expect_true(all(dplyr::filter(ou, Genotype == "a, b, c")[, c(2, 3)] ==

-                    c(1.3 * 1.5, 10 * 5)))

-    expect_true(all(dplyr::filter(ou, Genotype == "b, c, e")[, c(2, 3)] ==

-                    c(1.5 * 1.1, 5)))

-    expect_true(all(dplyr::filter(ou, Genotype == "a, b, c, e")[, c(2, 3)] ==

-                    c(1.3 * 1.5 * 1.1, 10 * 5)))

+    expect_equivalent(dplyr::filter(ou, Genotype == "a")[, c(2, 3)],

+                    c(1, 10))

+    expect_equivalent(dplyr::filter(ou, Genotype == "b")[, c(2, 3)],

+                    c(1, 1))

+    expect_equivalent(dplyr::filter(ou, Genotype == "c")[, c(2, 3)],

+                    c(1, 5))

+    expect_equivalent(dplyr::filter(ou, Genotype == "e")[, c(2, 3)],

+                    c(1.1, 1))

+    expect_equivalent(dplyr::filter(ou, Genotype == "a, b, c")[, c(2, 3)],

+                    c(1.3 * 1.5, 10 * 5))

+    expect_equivalent(dplyr::filter(ou, Genotype == "b, c, e")[, c(2, 3)],

+                    c(1.5 * 1.1, 5))

+    expect_equivalent(dplyr::filter(ou, Genotype == "a, b, c, e")[, c(2, 3)],

+                    c(1.3 * 1.5 * 1.1, 10 * 5))

     oo <- evalAllGenotypesFitAndMut(fe, fm)

-    expect_true(all(dplyr::filter(oo, Genotype == "a")[, c(2, 3)] ==

-                    c(1, 10)))

-    expect_true(all(dplyr::filter(oo, Genotype == "b")[, c(2, 3)] ==

-                    c(1, 1)))

-    expect_true(all(dplyr::filter(oo, Genotype == "c")[, c(2, 3)] ==

-                    c(1, 5)))

-    expect_true(all(dplyr::filter(oo, Genotype == "e")[, c(2, 3)] ==

-                    c(1.1, 1)))

-    expect_true(all(dplyr::filter(oo, Genotype == "a > b > c")[, c(2, 3)] ==

-                    c(1.3 * 1.5, 10 * 5)))

-    expect_true(all(dplyr::filter(oo, Genotype == "b > c > e")[, c(2, 3)] ==

-                    c(1.5 * 1.1, 5)))

-    expect_true(all(dplyr::filter(oo, Genotype == "e > b > c")[, c(2, 3)] ==

-                    c(1.5 * 1.1, 5)))

-    expect_true(all(dplyr::filter(oo, Genotype == "a > b > c > e")[, c(2, 3)] ==

-                    c(1.3 * 1.5 * 1.1, 10 * 5)))

+    expect_equivalent(dplyr::filter(oo, Genotype == "a")[, c(2, 3)],

+                    c(1, 10))

+    expect_equivalent(dplyr::filter(oo, Genotype == "b")[, c(2, 3)],

+                    c(1, 1))

+    expect_equivalent(dplyr::filter(oo, Genotype == "c")[, c(2, 3)],

+                    c(1, 5))

+    expect_equivalent(dplyr::filter(oo, Genotype == "e")[, c(2, 3)],

+                    c(1.1, 1))

+    expect_equivalent(dplyr::filter(oo, Genotype == "a > b > c")[, c(2, 3)],

+                    c(1.3 * 1.5, 10 * 5))

+    expect_equivalent(dplyr::filter(oo, Genotype == "b > c > e")[, c(2, 3)],

+                    c(1.5 * 1.1, 5))

+    expect_equivalent(dplyr::filter(oo, Genotype == "e > b > c")[, c(2, 3)],

+                    c(1.5 * 1.1, 5))

+    expect_equivalent(dplyr::filter(oo, Genotype == "a > b > c > e")[, c(2, 3)],

+                    c(1.3 * 1.5 * 1.1, 10 * 5))

 })

@@ -386,11 +386,11 @@ test_that("Mutator, several modules differences, fitness eval", {

                                     addwt = TRUE)

     e2 <- evalAllGenotypesFitAndMut(f1, mut2, order = FALSE,

                                     addwt = TRUE)

-    expect_true(all(e1$Fitness == rep(1, 64)))

-    expect_true(all(e1$MutatorFactor == c(1, rep(5, 63))))

-    expect_true(all(e2$Fitness == rep(1, 64)))

-    expect_true(

-        all(e2$MutatorFactor ==

+    expect_identical(e1$Fitness, rep(1, 64))

+    expect_identical(e1$MutatorFactor, c(1, rep(5, 63)))

+    expect_identical(e2$Fitness, rep(1, 64))

+    expect_identical(

+        e2$MutatorFactor,

                     c(1, rep(5, 7),

                       rep(25, 8), 5,

                       rep(25, 4), 5,

@@ -399,7 +399,7 @@ test_that("Mutator, several modules differences, fitness eval", {

                       rep(125, 4), rep(25, 6),

                       rep(125, 4), 25,

                       rep(125, 8), 25,

-                      rep(125, 7)))

+                      rep(125, 7))

     )

 })

 date()

@@ -1,15 +1,15 @@

 \usepackage[%

-		shash={d831b24},

-		lhash={d831b24426e21df39341f9b0930cfc8550d842a1},

-		authname={ramon diaz-uriarte (at Bufo)},

-		authemail={rdiaz02@gmail.com},

+		shash={3486983},

+		lhash={348698385e2f09528be7eb816768bd8ec06b7e70},

+		authname={Ramon Diaz-Uriarte},

+		authemail={rdiaz02@users.noreply.github.com},

 		authsdate={2016-06-23},

-		authidate={2016-06-23 17:39:18 +0200},

-		authudate={1466696358},

-		commname={ramon diaz-uriarte (at Bufo)},

-		commemail={rdiaz02@gmail.com},

+		authidate={2016-06-23 19:01:20 +0200},

+		authudate={1466701280},

+		commname={Ramon Diaz-Uriarte},

+		commemail={rdiaz02@users.noreply.github.com},

 		commsdate={2016-06-23},

-		commidate={2016-06-23 17:39:18 +0200},

-		commudate={1466696358},

-		refnames={ (HEAD -> master, origin/master, origin/HEAD)}

+		commidate={2016-06-23 19:01:20 +0200},

+		commudate={1466701280},

+		refnames={ (HEAD, origin/master, origin/HEAD)}

 	]{gitsetinfo}

\ No newline at end of file