Merge pull request datashield#651 from StuartWheater/v6.3.6-dev

Additional changes to v6.3.6-dev

Author: StuartWheater

.circleci/config.yml

@@ -6,7 +6,7 @@ jobs:
   dsbaseclient:
     docker:
 #      - image: cimg/base:current
-      - image: cimg/base:2024.11
+      - image: cimg/base:2026.02
     resource_class: small
     steps:
       - checkout

armadillo_azure-pipelines.yml

@@ -34,7 +34,7 @@ variables:
   branchName:  $(Build.SourceBranchName)
   test_filter: '*'
   _r_check_system_clock_: 0
-  PERF_PROFILE: 'azure-pipeline'
+  perf.profile: 'azure-pipeline'
 
 
 #########################################################################################
@@ -276,7 +276,7 @@ jobs:
       # "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
       # testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
 
-      sudo R -q -e '
+      sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
         library(covr);
         dsbase.res <- covr::package_coverage(
             type = c("none"),
@@ -398,7 +398,7 @@ jobs:
       # testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
       # R output and messages are redirected by sink() to test_console_output.txt
       # junit reporter output is to test_results.xml
-      sudo R -q -e '
+      sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
         library(covr);
         dsdanger.res <- covr::package_coverage(
             type = c("none"),

azure-pipelines.yml

@@ -32,7 +32,7 @@ variables:
   branchName:  $(Build.SourceBranchName)
   test_filter: '*'
   _r_check_system_clock_: 0
-  PERF_PROFILE: 'azure-pipeline'
+  perf.profile: 'azure-pipeline'
 
 
 #########################################################################################
@@ -255,7 +255,7 @@ jobs:
       # "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
       # testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
 
-      sudo R -q -e '
+      sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
         library(covr);
         dsbase.res <- covr::package_coverage(
             type = c("none"),
@@ -370,7 +370,7 @@ jobs:
       # testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
       # R output and messages are redirected by sink() to test_console_output.txt
       # junit reporter output is to test_results.xml
-      sudo R -q -e '
+      sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
         library(covr);
         dsdanger.res <- covr::package_coverage(
             type = c("none"),

opal_azure-pipelines.yml

@@ -34,7 +34,7 @@ variables:
   branchName:  $(Build.SourceBranchName)
   test_filter: '*'
   _r_check_system_clock_: 0
-  PERF_PROFILE: 'azure-pipeline'
+  perf.profile: 'azure-pipeline'
 
 
 #########################################################################################
@@ -274,7 +274,7 @@ jobs:
       # "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
       # testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
 
-      sudo R -q -e '
+      sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
         library(covr);
         dsbase.res <- covr::package_coverage(
             type = c("none"),
@@ -389,7 +389,7 @@ jobs:
       # testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
       # R output and messages are redirected by sink() to test_console_output.txt
       # junit reporter output is to test_results.xml
-      sudo R -q -e '
+      sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
         library(covr);
         dsdanger.res <- covr::package_coverage(
             type = c("none"),

tests/testthat/perf_files/dslite_hp-laptop-quay_perf-profile.csv

@@ -6,7 +6,7 @@
 "ds.asNumeric::perf:0","9.11018116242571","0.5","2"
 "ds.assign::perf::0","20.7627800741047","0.5","2"
 "ds.class::perf::combine:0","16.4968034024194","0.5","2"
-"ds.colnames::perf:0","12.2919611789594","0.5","2"
+"ds.colnames::perf:0","39.559281","0.5","2"
 "ds.exists::perf::combine:0","41.3622556042039","0.5","2"
 "ds.length::perf::combine:0","41.0818690662793","0.5","2"
 "ds.mean::perf::combine:0","40.9888639028757","0.5","2"

tests/testthat/perf_files/opal_hp-laptop-quay_perf-profile.csv

@@ -6,7 +6,7 @@
 "ds.asNumeric::perf:0","0.692813012683229","0.5","2"
 "ds.assign::perf::0","1.89351857736982","0.5","2"
 "ds.class::perf::combine:0","1.62870246867488","0.5","2"
-"ds.colnames::perf:0","1.32209430785405","0.5","2"
+"ds.colnames::perf:0","2.7125071","0.5","2"
 "ds.exists::perf::combine:0","3.45004426293124","0.5","2"
 "ds.length::perf::combine:0","2.78832377100152","0.5","2"
 "ds.mean::perf::combine:0","2.7801284055162","0.5","2"

tests/testthat/test-smk-ds.look.R

@@ -27,7 +27,7 @@ test_that("setup", {
 
 # context("ds.look::smk")
 test_that("simple look", {
-    res <- ds.look("lengthDS('D$LAB_TSC')")
+    res <- expect_warning(ds.look("lengthDS('D$LAB_TSC')"), "'ds.look' is deprecated.", fixed = TRUE)
 
     expect_length(res, 1)
     expect_length(res$output, 3)

tests/testthat/test-smk-ds.meanByClass.R

@@ -26,10 +26,11 @@ test_that("setup", {
 #
 
 # context("ds.meanByClass::smk::LAB_TSC across PM_BMI_CATEGORICAL categories where both vectors are 'loose'")
-ds.assign("D$LAB_TSC", "ldl")
-ds.assign("D$PM_BMI_CATEGORICAL", "pm_bmi")
 test_that("LAB_TSC_across_", {
-    res <- ds.meanByClass(x='ldl~pm_bmi')
+    ds.assign("D$LAB_TSC", "ldl")
+    ds.assign("D$PM_BMI_CATEGORICAL", "pm_bmi")
+
+    res <- expect_warning(ds.meanByClass(x='ldl~pm_bmi'), "'ds.meanByClass' is deprecated.", fixed = TRUE)
 
     expect_length(res, 6)
     expect_equal(res[[1]], '2753')
@@ -41,8 +42,8 @@ test_that("LAB_TSC_across_", {
 })
 
 # context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL across PM_BMI_CATEGORICAL categories")
-res <- ds.meanByClass(x='D', outvar='LAB_HDL', covar='PM_BMI_CATEGORICAL')
 test_that("LAB_HDL_across_PM_BMI_CATEGORICAL", {
+    res <- expect_warning(ds.meanByClass(x='D', outvar='LAB_HDL', covar='PM_BMI_CATEGORICAL'), "'ds.meanByClass' is deprecated.", fixed = TRUE)
 
     expect_length(res, 6)
     expect_equal(res[[1]], '2753')
@@ -55,8 +56,8 @@ test_that("LAB_HDL_across_PM_BMI_CATEGORICAL", {
 
 
 # context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL & LAB_TSC across bmi categories")
-res <- ds.meanByClass(x='D', outvar=c('LAB_HDL','LAB_TSC'), covar=c('PM_BMI_CATEGORICAL'))
 test_that("LAB_HDL-LAB_TSC_across_PM_BMI_CATEGORICAL", {
+    res <- expect_warning(ds.meanByClass(x='D', outvar=c('LAB_HDL','LAB_TSC'), covar=c('PM_BMI_CATEGORICAL')), "'ds.meanByClass' is deprecated.", fixed = TRUE)
 
     expect_length(res, 12)
     expect_equal(res[[1]], '2753')
@@ -77,10 +78,9 @@ test_that("LAB_HDL-LAB_TSC_across_PM_BMI_CATEGORICAL", {
 # context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL across gender bmi and diabetes status categories")
 # res <- ds.meanByClass(datasources=ds.test_env$connection.opal, x='D', outvar=c('LAB_HDL','LAB_TSC'), covar=c('GENDER','PM_BMI_CATEGORICAL','DIS_DIAB'))
 
-
 # context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL across PM_BMI_CATEGORICAL categories, split")
-res <- ds.meanByClass(x='D', outvar='LAB_HDL', covar='PM_BMI_CATEGORICAL', type='split')
 test_that("LAB_HDL_across_PM_BMI_CATEGORICAL", {
+    res <- expect_warning(ds.meanByClass(x='D', outvar='LAB_HDL', covar='PM_BMI_CATEGORICAL', type='split'), "'ds.meanByClass' is deprecated.", fixed = TRUE)
 
     expect_length(res, 3)
     expect_length(res$sim1, 6)

tests/testthat/test-smk-ds.message.R

@@ -28,7 +28,7 @@ test_that("setup", {
 
 # context("ds.message::smk")
 test_that("not exists - request message", {
-    message.res <- ds.message('Test')
+    message.res <- expect_warning(ds.message('Test'), "'ds.message' is deprecated.", fixed = TRUE)
 
     expect_length(message.res, 3)
     expect_equal(message.res$sim1, "Error: the object <message.object.name> does not exist in this datasource", fixed=TRUE)
@@ -39,7 +39,7 @@ test_that("not exists - request message", {
 test_that("exists - request message", {
     ds.list("D$LAB_TSC", "Test")
 
-    message.res <- ds.message('Test')
+    message.res <- expect_warning(ds.message('Test'), "'ds.message' is deprecated.", fixed = TRUE)
 
     expect_length(message.res, 3)
     expect_equal(message.res$sim1, "ALL OK: there are no studysideMessage(s) on this datasource", fixed=TRUE)
@@ -52,7 +52,7 @@ test_that("partial - request message - conn 1", {
 
     ds.list("D$LAB_TSC", newobj="TestP", datasources=ds.test_env$connections[1])
 
-    message.res <- ds.message('TestP')
+    message.res <- expect_warning(ds.message('TestP'), "'ds.message' is deprecated.", fixed = TRUE)
 
     expect_length(message.res, 3)
     expect_equal(message.res$sim1, "ALL OK: there are no studysideMessage(s) on this datasource", fixed=TRUE)
@@ -67,7 +67,7 @@ test_that("partial - request message - conn 2", {
 
     ds.list("D$LAB_TSC", newobj="TestP", datasources=ds.test_env$connections[2])
 
-    message.res <- ds.message('TestP')
+    message.res <- expect_warning(ds.message('TestP'), "'ds.message' is deprecated.", fixed = TRUE)
 
     expect_length(message.res, 3)
     expect_equal(message.res$sim1, "Error: the object <message.object.name> does not exist in this datasource", fixed=TRUE)
@@ -82,7 +82,7 @@ test_that("partial - request message - conn 3", {
 
     ds.list("D$LAB_TSC", newobj="TestP", datasources=ds.test_env$connections[3])
 
-    message.res <- ds.message('TestP')
+    message.res <- expect_warning(ds.message('TestP'), "'ds.message' is deprecated.", fixed = TRUE)
 
     expect_length(message.res, 3)
     expect_equal(message.res$sim1, "Error: the object <message.object.name> does not exist in this datasource", fixed=TRUE)

tests/testthat/test-smk-ds.subset.R

@@ -26,51 +26,57 @@ test_that("setup", {
 #
 
 # context("ds.subset::smk::generate a subset of the assigned table (by default the table is named 'D') with the first 50 observations and the two first columns")
-ds.subset(datasources=ds.test_env$connections, subset='subD', x='D', rows=c(1:50), cols=c(1,2))
-res <- ds.exists('subD')
 test_that("subD_exists", {
+    expect_warning(ds.subset(datasources=ds.test_env$connections, subset='subD', x='D', rows=c(1:50), cols=c(1,2)), "'ds.subset' is deprecated.", fixed = TRUE)
+
+    res <- ds.exists('subD')
+
     expect_length(res, 3)
     expect_true(res$sim1)
     expect_true(res$sim2)
     expect_true(res$sim3)
 })
 
 # context("ds.subset::smk::generate a subset of the assigned table (by default the table is named 'D') with the first 50 observations and the two first columns referred to by their names")
-ds.subset(subset='subD2', x='D', rows=c(1:50), cols = c('DIS_DIAB','PM_BMI_CONTINUOUS'))
-res <- ds.exists('subD2')
 test_that("subD2_exists", {
+    expect_warning(ds.subset(subset='subD2', x='D', rows=c(1:50), cols = c('DIS_DIAB','PM_BMI_CONTINUOUS')), "'ds.subset' is deprecated.", fixed = TRUE)
+
+    res <- ds.exists('subD2')
+
     expect_length(res, 3)
     expect_true(res$sim1)
     expect_true(res$sim2)
     expect_true(res$sim3)
 })
 
 # context("ds.subset::smk::generate a subset of the table D with bmi values greater than or equal to 25.")
-ds.subset(datasources=ds.test_env$connections, subset='subD3', x='D', logical='PM_BMI_CONTINUOUS>=', threshold=25)
-res <- ds.exists('subD3')
 test_that("subD3_exists", {
+    expect_warning(ds.subset(datasources=ds.test_env$connections, subset='subD3', x='D', logical='PM_BMI_CONTINUOUS>=', threshold=25), "'ds.subset' is deprecated.", fixed = TRUE)
+
+    res <- ds.exists('subD3')
+
     expect_length(res, 3)
     expect_true(res$sim1)
     expect_true(res$sim2)
     expect_true(res$sim3)
 })
 
 # context("ds.subset::smk::get the logarithmic values of the variable 'lab_hdl' and generate a subset with the first 50 observations of that new vector.")
-# ds.assign(toAssign='log(D$LAB_HDL)', newobj='logHDL')
-# ds.subset(datasources=ds.test_env$connections, subset="subLAB_HDL", x="logHDL", rows=c(1:50))
-# res <- ds.exists('subLAB_HDL')
 # test_that("subLAB_HDL_exists", {
+#     ds.assign(toAssign='log(D$LAB_HDL)', newobj='logHDL')
+#     ds.subset(datasources=ds.test_env$connections, subset="subLAB_HDL", x="logHDL", rows=c(1:50))
+#     res <- ds.exists('subLAB_HDL')
 #     expect_length(res, 3)
 #     expect_true(res$sim1)
 #     expect_true(res$sim2)
 #     expect_true(res$sim3)
 # })
 
 # context("ds.subset::smk::get the variable 'PM_BMI_CONTINUOUS' from the dataframe 'D' and generate a subset bmi vector with bmi values greater than or equal to 25")
-# ds.assign(toAssign='D$PM_BMI_CONTINUOUS', newobj='BMI')
-# ds.subset(datasources=ds.test_env$connections, subset='subBMI', x='BMI', logical='>=', threshold=25)
-# res <- ds.exists('subBMI')
 # test_that("subBMI_exists", {
+#     ds.assign(toAssign='D$PM_BMI_CONTINUOUS', newobj='BMI')
+#     ds.subset(datasources=ds.test_env$connections, subset='subBMI', x='BMI', logical='>=', threshold=25)
+#     res <- ds.exists('subBMI')
 #     expect_length(res, 3)
 #     expect_true(res$sim1)
 #     expect_true(res$sim2)