Browse code

2.99.2

ramon diaz-uriarte (at Phelsuma) authored on 11/12/2020 20:53:48
Showing7 changed files

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@@ -1,8 +1,8 @@
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 Package: OncoSimulR
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 Type: Package
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 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 
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-Version: 2.99.1
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-Date: 2020-12-10
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+Version: 2.99.2
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+Date: 2020-12-11
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 Authors@R: c(
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 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),	
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  	   		     email = "rdiaz02@gmail.com"),
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@@ -1,3 +1,6 @@
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+Changes in version 2.99.2 (2020-12-11):
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+	- Failed on test on Mac.
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+
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 Changes in version 2.99.1 (2020-12-10):
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 	- Bump version number for BioC, so it will become version 3.0.0 in
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           next release.
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new file mode 100644
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@@ -0,0 +1,6 @@
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+Many calls return warnings and that is expected. In many calls I do not
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+care about the warnings and thus I do not test for them (I am testing
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+other things). However, there is no way to have testthat ignore them (see
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+https://github.com/r-lib/testthat/issues/772 and
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+https://stackoverflow.com/questions/41165707/force-testthat-to-ignore-warnings).
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+That forces me to wrap that in "supressWarning". This is work in progress.
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@@ -30,8 +30,8 @@ test_that("We can run and equal with letters", {
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     ## It seems it is the Genotypes in the original Genotype spec.
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     ## but they are the ones left in fg1$Genotype
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     ## Since we cannot now what was in g1, do not allow for this.
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-    efg1 <- evalAllGenotypes(fg1, spPopSizes = c(9, 2, 6))
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-    efg11 <- evalAllGenotypes(fg11, spPopSizes = c(9, 2, 6))
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+    efg1 <- suppressWarnings(evalAllGenotypes(fg1, spPopSizes = c(9, 2, 6)))
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+    efg11 <- suppressWarnings(evalAllGenotypes(fg11, spPopSizes = c(9, 2, 6)))
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     expect_identical(efg1, efg11)
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     ## is that correct?
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@@ -48,16 +48,21 @@ test_that("We can run and equal with letters", {
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     fg1b <- allFitnessEffects(genotFitness = g1b, 
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                          frequencyDependentFitness = TRUE)
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     ## it thinks n_1_2 is 6. This is right
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-    (ea1b <- evalAllGenotypes(fg1b, spPopSizes = c(9, 2, 0, 6)))
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+
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+    (ea1b <- suppressWarnings(evalAllGenotypes(fg1b,
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+                                               spPopSizes = c(9, 2, 0, 6))))
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+    
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     ## is it correct? Yes
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     stopifnot(identical(ea1b[, "Fitness"], c(1, 1.3 + 1.2 * 6, 0, 1.1)))
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     set.seed(1)
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-    rfg1 <- oncoSimulIndiv(fg1, initMutant = "A", onlyCancer = FALSE, finalTime = 500, seed = NULL)
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+    rfg1 <- oncoSimulIndiv(fg1, initMutant = "A", onlyCancer = FALSE,
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+                           finalTime = 500, seed = NULL)
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     set.seed(1)
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-    rfg1b <- oncoSimulIndiv(fg1b, initMutant = "A", onlyCancer = FALSE, finalTime = 500, seed = NULL)
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+    rfg1b <- oncoSimulIndiv(fg1b, initMutant = "A", onlyCancer = FALSE,
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+                            finalTime = 500, seed = NULL)
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     expect_equivalent(rfg1, rfg1b)
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@@ -71,11 +76,13 @@ test_that("We can run and equal with letters", {
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     fg1c <- allFitnessEffects(genotFitness = g1c,
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                               frequencyDependentFitness = TRUE)
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     set.seed(1)
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-    rfg1c <- oncoSimulIndiv(fg1c, initMutant = "A", onlyCancer = FALSE, finalTime = 500, seed = NULL)
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+    rfg1c <- oncoSimulIndiv(fg1c, initMutant = "A", onlyCancer = FALSE,
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+                            finalTime = 500, seed = NULL)
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     expect_equivalent(rfg1, rfg1c)
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     set.seed(1)
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-    oncoSimulIndiv(fg1, initMutant = "A, B", onlyCancer = FALSE, finalTime = 500, seed = NULL)
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+    oncoSimulIndiv(fg1, initMutant = "A, B", onlyCancer = FALSE,
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+                   finalTime = 500, seed = NULL)
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 } )
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@@ -114,11 +114,12 @@ test_that("testing performance", {
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   expect_false(osi$FinalTime < 1.4)
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   expect_identical(osi$FinalTime, osi_ra$FinalTime)
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-  
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-  expect_equal(osi$NumIter, 458)
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-  
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+
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   expect_identical(osi$NumIter, osi_ra$NumIter)
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+  ## It fails on Mac. Well, the key is the identity below
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+  skip_on_os(c("mac"))
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+  expect_equal(osi$NumIter, 458)
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 })
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 test_that("testing Bozic failure", {
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@@ -50,6 +50,7 @@ MathJax.Hub.Config({
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 ```{r setup, include=FALSE}
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 ## use collapse for bookdown, to collapse all the source and output
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 ## blocks from one code chunk into a single block
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+time0 <- Sys.time()
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 knitr::opts_chunk$set(echo = TRUE, collapse = TRUE)
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 options(width = 70)
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 require(BiocStyle)
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@@ -13515,7 +13516,18 @@ This is the information about the version of R and packages used:
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 ```{r}
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 sessionInfo()
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 ``` 
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+Time to build the vignette:
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+
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+```{r last, echo=FALSE}
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+print(Sys.time() - time0)
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+```
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 \clearpage
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 # Funding
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 Supported by BFU2015-67302-R (MINECO/FEDER, EU) to
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 \usepackage[%
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-		shash={9937b8c},
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-		lhash={9937b8c186c58bc2625c357f9bc4cbc7d91cd5b7},
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+		shash={fc4cc14},
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+		lhash={fc4cc14670ae7a520669b0695c19dd2309aee59d},
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 		authname={ramon diaz-uriarte (at Phelsuma)},
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 		authemail={rdiaz02@gmail.com},
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-		authsdate={2020-12-09},
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-		authidate={2020-12-09 16:35:47 +0100},
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-		authudate={1607528147},
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+		authsdate={2020-12-10},
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+		authidate={2020-12-10 12:16:09 +0100},
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+		authudate={1607598969},
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 		commname={ramon diaz-uriarte (at Phelsuma)},
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 		commemail={rdiaz02@gmail.com},
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-		commsdate={2020-12-09},
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-		commidate={2020-12-09 16:35:47 +0100},
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-		commudate={1607528147},
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-		refnames={ (HEAD -> freq-dep-fitness, origin/initmutant, initmutant)}
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+		commsdate={2020-12-10},
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+		commidate={2020-12-10 12:16:09 +0100},
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+		commudate={1607598969},
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+		refnames={ (HEAD -> freq-dep-fitness)}
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 	]{gitsetinfo}
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