use skip_on_cran for some of test_loo_subsampling

need to get under CRAN timing limit

Author: jgabry

DESCRIPTION

@@ -2,7 +2,7 @@ Package: loo
 Type: Package
 Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models
 Version: 2.2.0
-Date: 2019-12-16
+Date: 2019-12-18
 Authors@R: c(person("Aki", "Vehtari", email = "[email protected]", role = c("aut")),
              person("Jonah", "Gabry", email = "[email protected]", role = c("cre", "aut")),
              person("Mans", "Magnusson", role = c("aut")),

tests/testthat/test_loo_approximate_posterior.R

@@ -49,7 +49,6 @@ for(j in 1:N){
 
 
 test_that("loo_approximate_posterior.array works as loo_approximate_posterior.matrix", {
-  skip_if_not_installed("checkmate")
 
   # Create array with two "chains"
   log_p_mat <- matrix(log_p, nrow = (S/2), ncol = 2)
@@ -86,7 +85,7 @@ test_that("loo_approximate_posterior.array works as loo_approximate_posterior.ma
 })
 
 test_that("loo_approximate_posterior.function works as loo_approximate_posterior.matrix", {
-  skip_if_not_installed("checkmate")
+
 
   # Compute aploo
   expect_silent(aploo1 <- loo_approximate_posterior.matrix(x = ll, log_p = log_p, log_g = log_g))

tests/testthat/test_loo_subsampling.R

@@ -4,8 +4,6 @@ options(mc.cores = 1)
 context("loo_subsampling")
 
 test_that("overall loo_subampling works as expected (compared with loo) for diff_est", {
-  skip_if_not_installed("checkmate")
-
   set.seed(123)
   N <- 1000; K <- 10; S <- 1000; a0 <- 3; b0 <- 2
   p <- 0.7
@@ -91,8 +89,6 @@ test_that("overall loo_subampling works as expected (compared with loo) for diff
 })
 
 test_that("loo with subsampling of all observations works as ordinary loo.", {
-  skip_if_not_installed("checkmate")
-
   set.seed(123)
   N <- 1000; K <- 10; S <- 1000; a0 <- 3; b0 <- 2
   p <- 0.7
@@ -122,8 +118,6 @@ test_that("loo with subsampling of all observations works as ordinary loo.", {
 })
 
 test_that("overall loo_subsample works with diff_srs as expected (compared with loo)", {
-  skip_if_not_installed("checkmate")
-
   set.seed(123)
   N <- 1000; K <- 10; S <- 1000; a0 <- 3; b0 <- 2
   p <- 0.7
@@ -143,8 +137,6 @@ test_that("overall loo_subsample works with diff_srs as expected (compared with
 })
 
 test_that("Test the srs estimator with 'none' approximation", {
-  skip_if_not_installed("checkmate")
-
   set.seed(123)
   N <- 1000; K <- 10; S <- 1000; a0 <- 3; b0 <- 2
   p <- 0.7
@@ -186,8 +178,6 @@ test_that("Test the srs estimator with 'none' approximation", {
 })
 
 test_that("Test the Hansen-Hurwitz estimator", {
-  skip_if_not_installed("checkmate")
-
   set.seed(123)
   N <- 1000; K <- 10; S <- 1000; a0 <- 3; b0 <- 2
   p <- 0.7
@@ -245,7 +235,7 @@ test_that("Test the Hansen-Hurwitz estimator", {
 
 
 test_that("update.psis_loo_ss works as expected (compared with loo)", {
-  skip_if_not_installed("checkmate")
+
 
   set.seed(123)
   N <- 1000; K <- 10; S <- 1000; a0 <- 3; b0 <- 2
@@ -344,7 +334,7 @@ test_that("update.psis_loo_ss works as expected (compared with loo)", {
 context("loo_subsampling_approximations")
 
 test_that("elpd_loo_approximation works as expected", {
-  skip_if_not_installed("checkmate")
+
 
   set.seed(123)
   N <- 10; K <- 10; S <- 1000; a0 <- 3; b0 <- 2
@@ -396,7 +386,7 @@ test_that("elpd_loo_approximation works as expected", {
 
 
 test_that("Test loo_approximation_draws", {
-  skip_if_not_installed("checkmate")
+
 
   set.seed(123)
   N <- 1000; K <- 10; S <- 1000; a0 <- 3; b0 <- 2
@@ -432,7 +422,7 @@ test_that("Test loo_approximation_draws", {
 
 
 test_that("waic using delta method and gradient", {
-  skip_if_not_installed("checkmate")
+
 
   if (FALSE){
     # Code to generate testdata - saved and loaded to avoid dependency of mvtnorm
@@ -488,7 +478,7 @@ test_that("waic using delta method and gradient", {
 })
 
 test_that("waic using delta 2nd order method", {
-  skip_if_not_installed("checkmate")
+
 
   if (FALSE){
     # Code to generate testdata - saved and loaded to avoid dependency of MCMCPack
@@ -575,7 +565,7 @@ test_that("waic using delta 2nd order method", {
 context("loo_subsampling_estimation")
 
 test_that("whhest works as expected", {
-  skip_if_not_installed("checkmate")
+
 
   N <- 100
   m <- 10
@@ -636,7 +626,7 @@ test_that("whhest works as expected", {
 
 
 test_that("srs_diff_est works as expected", {
-  skip_if_not_installed("checkmate")
+
 
   set.seed(1234)
   N <- 1000
@@ -672,7 +662,7 @@ test_that("srs_diff_est works as expected", {
 })
 
 test_that("srs_est works as expected", {
-  skip_if_not_installed("checkmate")
+
 
   set.seed(1234)
   # Cochran 1976 example Table 2.2
@@ -725,7 +715,8 @@ test_that("srs_est works as expected", {
 context("loo_subsampling cases")
 
 test_that("Test loo_subsampling and loo_approx with radon data", {
-  skip_if_not_installed("checkmate")
+  skip_on_cran() # avoid going over time limit for tests
+
   load(test_path("test_radon_laplace_loo.rda"))
   # Rename to spot variable leaking errors
   llfun_test <- llfun
@@ -833,13 +824,14 @@ test_that("Test loo_subsampling and loo_approx with radon data", {
 
 
 test_that("Test the vignette", {
-  skip_if_not_installed("checkmate")
+  skip_on_cran()
+
 
   # NOTE
   # If any of these test fails, the vignette probably needs to be updated
 
-  if (FALSE){
-    # Generate vignett test case
+  if (FALSE) {
+    # Generate vignette test case
     library("rstan")
     stan_code <- "
     data {
@@ -986,7 +978,7 @@ test_that("Test the vignette", {
 context("loo_compare_subsample")
 
 test_that("loo_compare_subsample", {
-  skip_if_not_installed("checkmate")
+  skip_on_cran() # to get under cran check time limit
 
   set.seed(123)
   N <- 1000
@@ -1067,9 +1059,10 @@ test_that("loo_compare_subsample", {
 
 })
 
+context("subsample with tis, sis")
 
 test_that("Test 'tis' and 'sis'", {
-  skip_if_not_installed("checkmate")
+  skip_on_cran()
 
   set.seed(123)
   N <- 1000; K <- 10; S <- 1000; a0 <- 3; b0 <- 2
@@ -1160,6 +1153,3 @@ test_that("Test 'tis' and 'sis'", {
   expect_gt(loo_ss_sis_S10$estimates["elpd_loo", "Estimate"] + SEs*loo_ss_sis_S10$estimates["elpd_loo", "subsampling SE"], loo_ss_full$estimates["elpd_loo", "Estimate"])
   expect_lt(loo_ss_sis_S10$estimates["elpd_loo", "Estimate"] - SEs*loo_ss_sis_S10$estimates["elpd_loo", "subsampling SE"], loo_ss_full$estimates["elpd_loo", "Estimate"])
 })
-
-
-

tests/testthat/test_psis_approximate_posterior.R

@@ -5,7 +5,6 @@ context("psis_approximate_posterior")
 load(test_path("test_data_psis_approximate_posterior.rda"))
 
 test_that("Laplace approximation, independent posterior", {
-  skip_if_not_installed("checkmate")
   log_p <- test_data_psis_approximate_posterior$laplace_independent$log_p
   log_g <- test_data_psis_approximate_posterior$laplace_independent$log_q
   ll <- test_data_psis_approximate_posterior$laplace_independent$log_liks
@@ -26,7 +25,6 @@ test_that("Laplace approximation, independent posterior", {
 
 
 test_that("Laplace approximation, correlated posterior", {
-  skip_if_not_installed("checkmate")
   log_p <- test_data_psis_approximate_posterior$laplace_correlated$log_p
   log_g <- test_data_psis_approximate_posterior$laplace_correlated$log_q
   ll <- test_data_psis_approximate_posterior$laplace_correlated$log_liks
@@ -46,7 +44,6 @@ test_that("Laplace approximation, correlated posterior", {
 })
 
 test_that("Laplace approximation, normal model", {
-  skip_if_not_installed("checkmate")
   log_p <- test_data_psis_approximate_posterior$laplace_normal$log_p
   log_g <- test_data_psis_approximate_posterior$laplace_normal$log_q
   ll <- test_data_psis_approximate_posterior$laplace_normal$log_liks
@@ -68,7 +65,6 @@ test_that("Laplace approximation, normal model", {
 
 
 test_that("ADVI fullrank approximation, independent posterior", {
-  skip_if_not_installed("checkmate")
   log_p <- test_data_psis_approximate_posterior$fullrank_independent$log_p
   log_g <- test_data_psis_approximate_posterior$fullrank_independent$log_q
   ll <- test_data_psis_approximate_posterior$fullrank_independent$log_liks
@@ -89,7 +85,6 @@ test_that("ADVI fullrank approximation, independent posterior", {
 
 
 test_that("ADVI fullrank approximation, correlated posterior", {
-  skip_if_not_installed("checkmate")
   log_p <- test_data_psis_approximate_posterior$fullrank_correlated$log_p
   log_g <- test_data_psis_approximate_posterior$fullrank_correlated$log_q
   ll <- test_data_psis_approximate_posterior$fullrank_correlated$log_liks
@@ -109,7 +104,6 @@ test_that("ADVI fullrank approximation, correlated posterior", {
 })
 
 test_that("ADVI fullrank approximation, correlated posterior", {
-  skip_if_not_installed("checkmate")
   log_p <- test_data_psis_approximate_posterior$fullrank_normal$log_p
   log_g <- test_data_psis_approximate_posterior$fullrank_normal$log_q
   ll <- test_data_psis_approximate_posterior$fullrank_normal$log_liks
@@ -130,7 +124,6 @@ test_that("ADVI fullrank approximation, correlated posterior", {
 
 
 test_that("ADVI meanfield approximation, independent posterior", {
-  skip_if_not_installed("checkmate")
   log_p <- test_data_psis_approximate_posterior$meanfield_independent$log_p
   log_g <- test_data_psis_approximate_posterior$meanfield_independent$log_q
   ll <- test_data_psis_approximate_posterior$meanfield_independent$log_liks
@@ -151,7 +144,6 @@ test_that("ADVI meanfield approximation, independent posterior", {
 
 
 test_that("ADVI meanfield approximation, correlated posterior", {
-  skip_if_not_installed("checkmate")
   log_p <- test_data_psis_approximate_posterior$meanfield_correlated$log_p
   log_g <- test_data_psis_approximate_posterior$meanfield_correlated$log_q
   ll <- test_data_psis_approximate_posterior$meanfield_correlated$log_liks
@@ -172,7 +164,6 @@ test_that("ADVI meanfield approximation, correlated posterior", {
 })
 
 test_that("ADVI meanfield approximation, normal model", {
-  skip_if_not_installed("checkmate")
   log_p <- test_data_psis_approximate_posterior$meanfield_normal$log_p
   log_g <- test_data_psis_approximate_posterior$meanfield_normal$log_q
   ll <- test_data_psis_approximate_posterior$meanfield_normal$log_liks
@@ -193,7 +184,7 @@ test_that("ADVI meanfield approximation, normal model", {
 
 
 test_that("ADVI meanfield approximation, normal model", {
-  skip_if_not_installed("checkmate")
+
   log_p <- test_data_psis_approximate_posterior$meanfield_normal$log_p
   log_g <- test_data_psis_approximate_posterior$meanfield_normal$log_q
   ll <- test_data_psis_approximate_posterior$meanfield_normal$log_liks
@@ -214,7 +205,7 @@ test_that("ADVI meanfield approximation, normal model", {
 
 
 test_that("Deprecation of log_q argument", {
-  skip_if_not_installed("checkmate")
+
   log_p <- test_data_psis_approximate_posterior$laplace_independent$log_p
   log_g <- test_data_psis_approximate_posterior$laplace_independent$log_q
   ll <- test_data_psis_approximate_posterior$laplace_independent$log_liks