From 120aba790757ab411abe7f62e8fa7383b897db22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= Date: Mon, 14 Jul 2025 16:39:28 -0400 Subject: [PATCH 1/4] small updates --- tests/testthat/helper-objects.R | 5 ++--- tests/testthat/test-spark-boost-tree.R | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/tests/testthat/helper-objects.R b/tests/testthat/helper-objects.R index 52db3419..1420a578 100644 --- a/tests/testthat/helper-objects.R +++ b/tests/testthat/helper-objects.R @@ -19,13 +19,12 @@ run_glmnet <- utils::compareVersion('3.6.0', as.character(getRversion())) > 0 spark_not_installed <- function() { - quietly_inquire_re_spark <- purrr:::quietly(sparklyr::spark_install_find)() - need_install <- try(quietly_inquire_re_spark(), silent = TRUE) + need_install <- purrr:::quietly(sparklyr::spark_install_find)() if(inherits(need_install, "try-error")) { need_install <- TRUE } else { - need_install <- !isTRUE(need_install$installed) + need_install <- !isTRUE(need_install$result$installed) } need_install } diff --git a/tests/testthat/test-spark-boost-tree.R b/tests/testthat/test-spark-boost-tree.R index 1c5fed3f..e865e215 100644 --- a/tests/testthat/test-spark-boost-tree.R +++ b/tests/testthat/test-spark-boost-tree.R @@ -1,5 +1,5 @@ ## Skip entire file is Spark is not installed -skip_if(spark_not_installed) +skip_if(spark_not_installed()) library(testthat) library(parsnip) From 465fee8ab594669f5b0968adcc7db7c039f91ac8 Mon Sep 17 00:00:00 2001 From: topepo Date: Tue, 15 Jul 2025 13:35:03 -0400 Subject: [PATCH 2/4] suggestions for Edgar --- .github/workflows/spark-R-CMD-check.yaml | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/.github/workflows/spark-R-CMD-check.yaml b/.github/workflows/spark-R-CMD-check.yaml index 60782eaa..b377f211 100644 --- a/.github/workflows/spark-R-CMD-check.yaml +++ b/.github/workflows/spark-R-CMD-check.yaml @@ -39,12 +39,6 @@ jobs: - uses: r-lib/actions/setup-pandoc@v2 - - uses: actions/setup-java@v1 - with: - java-version: '8' # The JDK version to make available on the path. - java-package: jdk # (jre, jdk, or jdk+fx) - defaults to jdk - architecture: x64 # (x64 or x86) - defaults to x64 - - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} @@ -63,7 +57,7 @@ jobs: - name: Install Spark run: | - try(sparklyr::spark_install(verbose = TRUE), silent = TRUE) + try(sparklyr::spark_install(version = "3.4.0", verbose = TRUE), silent = TRUE) shell: Rscript {0} - name: Install devel versions From 1f08d107ad9efd42010dbd6d08b29dbce999bf55 Mon Sep 17 00:00:00 2001 From: topepo Date: Tue, 15 Jul 2025 14:47:07 -0400 Subject: [PATCH 3/4] temporarily go back to v1.9.0 to see if it fails --- DESCRIPTION | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 985a42eb..aefb128c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -74,7 +74,8 @@ Suggests: yardstick Remotes: mixOmicsTeam/mixOmics, - r-lib/pillar + r-lib/pillar, + sparklyr/sparklyr@v1.9.0 biocViews: mixOmics Config/testthat/edition: 3 Config/testthat/start-first: parsnip-extension-messaging From 2c8030c49e252d5c5b408a03b2b6d93a9594fd5d Mon Sep 17 00:00:00 2001 From: topepo Date: Wed, 30 Jul 2025 12:33:47 -0400 Subject: [PATCH 4/4] update tests to use dev sparklyr --- DESCRIPTION | 3 +-- tests/testthat/test-parsnip-case-weights.R | 9 +++++---- tests/testthat/test-spark-boost-tree.R | 14 ++++++++++++++ tests/testthat/test-spark-data-descriptors.R | 1 + tests/testthat/test-spark-linear-reg.R | 1 + tests/testthat/test-spark-logistic-reg.R | 1 + tests/testthat/test-spark-multinom-reg.R | 1 + tests/testthat/test-spark-rand-forest.R | 1 + 8 files changed, 25 insertions(+), 6 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index aefb128c..985a42eb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -74,8 +74,7 @@ Suggests: yardstick Remotes: mixOmicsTeam/mixOmics, - r-lib/pillar, - sparklyr/sparklyr@v1.9.0 + r-lib/pillar biocViews: mixOmics Config/testthat/edition: 3 Config/testthat/start-first: parsnip-extension-messaging diff --git a/tests/testthat/test-parsnip-case-weights.R b/tests/testthat/test-parsnip-case-weights.R index 450c27ba..c0e973bb 100644 --- a/tests/testthat/test-parsnip-case-weights.R +++ b/tests/testthat/test-parsnip-case-weights.R @@ -1,9 +1,10 @@ # theses are needed for all case-weights tests skip_if_not_installed("parsnip", "1.0.1") -skip_if_not_installed("hardhat", "1.2.0") -skip_if_not_installed("yardstick", "1.0.0") -skip_if_not_installed("workflows", "1.0.0") -skip_if_not_installed("recipes", "1.0.0") +skip_if_not_installed("hardhat", minimum_version = "1.2.0") +skip_if_not_installed("yardstick", minimum_version = "1.0.0") +skip_if_not_installed("workflows", minimum_version = "1.0.0") +skip_if_not_installed("recipes", minimum_version = "1.0.0") +skip_if_not_installed("sparklyr", minimum_version = "1.9.1.9000") # load all extension packages to register the engines library(parsnip) diff --git a/tests/testthat/test-spark-boost-tree.R b/tests/testthat/test-spark-boost-tree.R index e865e215..0dafe6e8 100644 --- a/tests/testthat/test-spark-boost-tree.R +++ b/tests/testthat/test-spark-boost-tree.R @@ -1,5 +1,6 @@ ## Skip entire file is Spark is not installed skip_if(spark_not_installed()) +skip_if_not_installed("sparklyr", minimum_version = "1.9.1.9000") library(testthat) library(parsnip) @@ -11,6 +12,19 @@ hpc <- hpc_data[1:150, c(2:5, 8)] # ------------------------------------------------------------------------------ +test_that('Reminder to check for CRAN sparklyr > 1.9.1.9000', { + + check_spark_version <- packageVersion("sparklyr") < "1.9.2" + check_time <- Sys.Date() >= as.Date("2025-09-01") + + time_to_look_for_new_sparklyr_version <- check_spark_version & check_time + + expect_false(time_to_look_for_new_sparklyr_version) + +}) + + + test_that('spark execution', { skip_if_not_installed("sparklyr") diff --git a/tests/testthat/test-spark-data-descriptors.R b/tests/testthat/test-spark-data-descriptors.R index b2ab3004..578799cb 100644 --- a/tests/testthat/test-spark-data-descriptors.R +++ b/tests/testthat/test-spark-data-descriptors.R @@ -1,5 +1,6 @@ ## Skip entire file is Spark is not installed skip_if(spark_not_installed()) +skip_if_not_installed("sparklyr", minimum_version = "1.9.1.9000") library(testthat) library(parsnip) diff --git a/tests/testthat/test-spark-linear-reg.R b/tests/testthat/test-spark-linear-reg.R index 33783b81..a6d9422a 100644 --- a/tests/testthat/test-spark-linear-reg.R +++ b/tests/testthat/test-spark-linear-reg.R @@ -1,5 +1,6 @@ ## Skip entire file is Spark is not installed skip_if(spark_not_installed()) +skip_if_not_installed("sparklyr", minimum_version = "1.9.1.9000") library(testthat) library(parsnip) diff --git a/tests/testthat/test-spark-logistic-reg.R b/tests/testthat/test-spark-logistic-reg.R index 3843555d..54e0c237 100644 --- a/tests/testthat/test-spark-logistic-reg.R +++ b/tests/testthat/test-spark-logistic-reg.R @@ -1,5 +1,6 @@ ## Skip entire file is Spark is not installed skip_if(spark_not_installed()) +skip_if_not_installed("sparklyr", minimum_version = "1.9.1.9000") library(testthat) library(parsnip) diff --git a/tests/testthat/test-spark-multinom-reg.R b/tests/testthat/test-spark-multinom-reg.R index 7fe46436..20b9ed6b 100644 --- a/tests/testthat/test-spark-multinom-reg.R +++ b/tests/testthat/test-spark-multinom-reg.R @@ -1,5 +1,6 @@ ## Skip entire file is Spark is not installed skip_if(spark_not_installed()) +skip_if_not_installed("sparklyr", minimum_version = "1.9.1.9000") library(testthat) library(parsnip) diff --git a/tests/testthat/test-spark-rand-forest.R b/tests/testthat/test-spark-rand-forest.R index 05db82d0..6a299f7e 100644 --- a/tests/testthat/test-spark-rand-forest.R +++ b/tests/testthat/test-spark-rand-forest.R @@ -1,5 +1,6 @@ ## Skip entire file is Spark is not installed skip_if(spark_not_installed()) +skip_if_not_installed("sparklyr", minimum_version = "1.9.1.9000") library(testthat) library(parsnip)