Simplfy pipeline

Author: StuartWheater

azure-pipelines.yml

@@ -116,7 +116,7 @@ jobs:
       sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
       sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
       sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
-      sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
+      sudo R -q -e "install.packages(c('devtools'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
@@ -256,31 +256,11 @@ jobs:
       # testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
 
       sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
-        library(covr);
-        dsbase.res <- covr::package_coverage(
-            type = c("none"),
-            code = c(
-                '"'"'
-                library(testthat);
-                output_file <- file("test_console_output_dsbase.txt");
-                sink(output_file);
-                sink(output_file, type = "message");
-                library(testthat);
-                junit_rep <- JunitReporter$new(file = "test_results_dsbase.xml");
-                progress_rep <- ProgressReporter$new(max_failures = 999999);
-                multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
-                options("datashield.return_errors" = FALSE);
-                options("default_driver" = "OpalDriver");
-                testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
-                '"'"'
-            )
-        );
-        base::saveRDS(dsbase.res, "test_results_dsbase.rds")'
-
-      # display the test console output
-      cat test_console_output_dsbase.txt
-
-      grep --quiet " FAIL 0 " test_console_output_dsbase.txt
+          library(testthat);
+          progress_rep <- ProgressReporter$new(max_failures = 999999);
+          multi_rep    <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
+          options("default_driver" = "OpalDriver");
+          testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)'
 
     workingDirectory: $(Pipeline.Workspace)/dsBaseClient
     displayName: 'Code coverage and JUnit report output, with dsBase'