git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@109194 bc3139a8-67e5-0310-9ffc-ced21a209358
Ramon Diaz-Uriarte authored on 05/10/2015 14:03:58
| ... | ... |
@@ -1,17 +1,14 @@ |
| 1 | 1 |
test_that("oncoSimulSample out of time triggered", {
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- |
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| 3 | 2 |
oi <- allFitnessEffects(orderEffects = |
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- c("F > D" = -0.3, "D > F" = 0.4),
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+ c("F > D" = -0.3, "D > F" = 0.1),
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| 5 | 4 |
noIntGenes = rexp(5, 10), |
| 6 | 5 |
geneToModule = |
| 7 | 6 |
c("Root" = "Root",
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| 8 | 7 |
"F" = "f1, f2, f3", |
| 9 | 8 |
"D" = "d1, d2") ) |
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- |
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- expect_message(out <- oncoSimulSample(100, oi, |
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+ expect_message(out <- oncoSimulSample(5000, oi, |
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| 12 | 10 |
max.wall.time.total = 1), |
| 13 | 11 |
"Run out of time") |
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- |
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| 15 | 12 |
expect_true(out$HittedWallTime) |
| 16 | 13 |
}) |
| 17 | 14 |
|
| ... | ... |
@@ -26,7 +23,7 @@ test_that("oncoSimulSample out of time triggered, 2", {
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| 26 | 23 |
s = 0.05, |
| 27 | 24 |
sh = -0.3, |
| 28 | 25 |
typeDep = "MN")) |
| 29 |
- expect_message(out <- oncoSimulSample(100, pancr, |
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+ expect_message(out <- oncoSimulSample(5000, pancr, |
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| 30 | 27 |
max.wall.time.total = 1), |
| 31 | 28 |
"Run out of time") |
| 32 | 29 |
expect_true(out$HittedWallTime) |
| ... | ... |
@@ -36,14 +33,14 @@ test_that("oncoSimulSample out of time triggered, 2", {
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| 36 | 33 |
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| 37 | 34 |
test_that("oncoSimulSample out of attempts triggered", {
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| 38 | 35 |
oi <- allFitnessEffects(orderEffects = |
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- c("F > D" = -0.3, "D > F" = 0.4),
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+ c("F > D" = -0.3, "D > F" = 0.05),
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| 40 | 37 |
noIntGenes = rexp(5, 10), |
| 41 | 38 |
geneToModule = |
| 42 | 39 |
c("Root" = "Root",
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| 43 | 40 |
"F" = "f1, f2, f3", |
| 44 | 41 |
"D" = "d1, d2") ) |
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- expect_message(out <- oncoSimulSample(10, oi, |
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- max.num.tries.total = 11), |
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+ expect_message(out <- oncoSimulSample(5000, oi, |
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+ max.num.tries.total = 5001), |
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| 47 | 44 |
"Run out of attempts (in C++)", fixed = TRUE) |
| 48 | 45 |
expect_true(out$HittedMaxTries) |
| 49 | 46 |
}) |
| ... | ... |
@@ -57,8 +54,8 @@ test_that("oncoSimulSample out of attempts triggered, 2", {
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| 57 | 54 |
s = 0.05, |
| 58 | 55 |
sh = -0.3, |
| 59 | 56 |
typeDep = "MN")) |
| 60 |
- expect_message(out <- oncoSimulSample(10, pancr, |
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- max.num.tries.total = 12), |
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+ expect_message(out <- oncoSimulSample(5000, pancr, |
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+ max.num.tries.total = 5002), |
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| 62 | 59 |
"Run out of attempts (in C++)", fixed = TRUE) |
| 63 | 60 |
expect_true(out$HittedMaxTries) |
| 64 | 61 |
}) |
| ... | ... |
@@ -79,13 +76,14 @@ test_that("oncoSimulSample out of time in C++ triggered", {
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| 79 | 76 |
s = 0.05, |
| 80 | 77 |
sh = -0.3, |
| 81 | 78 |
typeDep = "MN")) |
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- |
|
| 83 | 79 |
expect_message(out <- oncoSimulSample(1, pancr, "McFL", |
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- detectionSize = 1e9, |
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- detectionDrivers = 4, |
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- max.wall.time.total = 0.5), |
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+ detectionSize = 1e9, |
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+ detectionDrivers = 6, |
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+ initSize = 50, |
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+ finalTime = 10000, |
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+ sampleEvery = 0.005, |
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+ max.wall.time.total = 1), |
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| 87 | 86 |
"Run out of time (in C++)", fixed = TRUE) |
| 88 |
- |
|
| 89 | 87 |
expect_true(out$HittedWallTime) |
| 90 | 88 |
}) |
| 91 | 89 |
|
| ... | ... |
@@ -1,15 +1,15 @@ |
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\usepackage[% |
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- shash={b9add94},
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- lhash={b9add94a80c0037d5de904c87757f6a1ce79f444},
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+ shash={39be2bc},
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+ lhash={39be2bc525ceffa46743bd5fd80cde0c1f959434},
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authname={Ramon Diaz-Uriarte (at Coleonyx)},
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| 5 | 5 |
authemail={rdiaz02@gmail.com},
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- authsdate={2015-10-02},
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- authidate={2015-10-02 16:21:37 +0200},
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- authudate={1443795697},
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+ authsdate={2015-10-05},
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+ authidate={2015-10-05 00:56:02 +0200},
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+ authudate={1443999362},
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commname={Ramon Diaz-Uriarte (at Coleonyx)},
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| 10 | 10 |
commemail={rdiaz02@gmail.com},
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- commsdate={2015-10-02},
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- commidate={2015-10-02 16:21:37 +0200},
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- commudate={1443795697},
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+ commsdate={2015-10-05},
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+ commidate={2015-10-05 00:56:02 +0200},
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+ commudate={1443999362},
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refnames={ (HEAD -> master)}
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| 15 | 15 |
]{gitsetinfo}
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| 16 | 16 |
\ No newline at end of file |