diff --git a/.circleci/config.yml b/.circleci/config.yml index ec6d40e9..7ee4e084 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -26,22 +26,8 @@ jobs: - run: command: | echo "options(Ncpus=4)" >> ~/.Rprofile - sudo Rscript -e "install.packages('RANN', dependencies=TRUE)" - sudo Rscript -e "install.packages('stringr', dependencies=TRUE)" - sudo Rscript -e "install.packages('lme4', dependencies=TRUE)" - sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)" - sudo Rscript -e "install.packages('reshape2', dependencies=TRUE)" - sudo Rscript -e "install.packages('polycor', dependencies=TRUE)" - sudo Rscript -e "install.packages('splines', dependencies=TRUE)" - sudo Rscript -e "install.packages('gamlss', dependencies=TRUE)" - sudo Rscript -e "install.packages('gamlss.dist', dependencies=TRUE)" - sudo Rscript -e "install.packages('mice', dependencies=TRUE)" - sudo Rscript -e "install.packages('childsds', dependencies=TRUE)" - sudo Rscript -e "install.packages('xml2', dependencies=TRUE)" - sudo Rscript -e "install.packages('covr', dependencies=TRUE)" - sudo Rscript -e "install.packages('devtools', dependencies=TRUE)" - sudo Rscript -e "install.packages('DSI', dependencies=TRUE)" - sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)" + + sudo R -q -e "options(repos=c(CRAN=paste0('https://packagemanager.posit.co/cran/__linux__/', system('lsb_release -cs', intern=TRUE), '/latest')), HTTPUserAgent=sprintf('R/%s R (%s)', getRversion(), paste(getRversion(), R.version\$platform, R.version\$arch, R.version\$os)), Ncpus=4); install.packages(c('devtools','RANN','stringr','lme4','dplyr','reshape2','polycor','splines','gamlss','gamlss.dist','mice','data.table','childsds'), dependencies=TRUE)" - run: command: | sudo Rscript -e 'library(covr); covr::codecov(token = "'$CODECOV_TOKEN'")' diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 94c767e9..77679f06 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -27,8 +27,7 @@ variables: branchName: $(Build.SourceBranchName) test_filter: '*' _r_check_system_clock_: 0 - PERF_PROFILE: 'azure-pipeline' - + perf.profile: 'azure-pipeline' ######################################################################################### @@ -50,13 +49,13 @@ schedules: displayName: Weekly build - latest release branches: include: - - 6.3.4 + - 6.3.5 always: true - cron: "0 1 * * *" displayName: Nightly build - development branchs branches: include: - - v6.3.5-dev + - v6.3.6-dev - v6.4.0-dev - v7.0.0-dev always: true @@ -184,7 +183,7 @@ jobs: # R output and messages are redirected by sink() to test_console_output.txt # junit reporter output is to test_results.xml - sudo R -q -e ' + sudo env PERF_PROFILE=$PERF_PROFILE R -q -e ' library(covr); write.csv( coverage_to_list( diff --git a/tests/testthat/perf_files/azure-pipeline_perf-profile.csv b/tests/testthat/perf_files/azure-pipeline_perf-profile.csv index 77f556bc..5267505e 100644 --- a/tests/testthat/perf_files/azure-pipeline_perf-profile.csv +++ b/tests/testthat/perf_files/azure-pipeline_perf-profile.csv @@ -1,5 +1,5 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"meanDS::perf::numeric::0","2998.9844","0.5","2" -"meanDS::perf::numberAndNA::0","3027.3963","0.5","2" -"varDS::perf::numeric::0","3124.4088","0.5","2" -"varDS::perf::numberAndNA::0","3146.532","0.5","2" +"meanDS::perf::numeric::0","4497.0","0.5","2" +"meanDS::perf::numberAndNA::0","4542.0","0.5","2" +"varDS::perf::numeric::0","6373.0","0.5","2" +"varDS::perf::numberAndNA::0","4500.0","0.5","2" diff --git a/tests/testthat/test-perf-meanDS.R b/tests/testthat/test-perf-meanDS.R index 53e4c7af..c8ecf405 100644 --- a/tests/testthat/test-perf-meanDS.R +++ b/tests/testthat/test-perf-meanDS.R @@ -26,7 +26,7 @@ set.standard.disclosure.settings() # context("meanDS::perf::numeric") test_that("numeric meanDS - performance", { - skip_on_cran() +# skip_on_cran() input <- c(0.0, 1.0, 2.0, 3.0, 4.0) @@ -45,10 +45,10 @@ test_that("numeric meanDS - performance", { .current.rate <- .count / (difftime(.current.time, .start.time, units = "secs")[[1]]) .reference.rate <- perf.reference.rate("meanDS::perf::numeric::0") if (any(length(.reference.rate) == 0) || any(is.null(.reference.rate))) { - print(paste("meanDS::perf::numeric::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper())) + write(paste("meanDS::perf::numeric::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()), stderr()) perf.reference.save("meanDS::perf::numeric::0", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()) } else { - print(paste("meanDS::perf::numeric::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = '')) + write(paste("meanDS::perf::numeric::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''), stderr()) } .reference.rate <- perf.reference.rate("meanDS::perf::numeric::0") @@ -61,7 +61,7 @@ test_that("numeric meanDS - performance", { # context("meanDS::perf::numeric with NA") test_that("numeric meanDS, with NA - performance", { - skip_on_cran() +# skip_on_cran() input <- c(0.0, NA, 2.0, NA, 4.0) @@ -80,10 +80,10 @@ test_that("numeric meanDS, with NA - performance", { .current.rate <- .count / (difftime(.current.time, .start.time, units = "secs")[[1]]) .reference.rate <- perf.reference.rate("meanDS::perf::numberAndNA::0") if (any(length(.reference.rate) == 0) || any(is.null(.reference.rate))) { - print(paste("meanDS::perf::numberAndNA::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper())) + write(paste("meanDS::perf::numberAndNA::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()), stderr()) perf.reference.save("meanDS::perf::numberAndNA::0", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()) } else { - print(paste("meanDS::perf::numberAndNA::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = '')) + write(paste("meanDS::perf::numberAndNA::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''), stderr()) } .reference.rate <- perf.reference.rate("meanDS::perf::numberAndNA::0") diff --git a/tests/testthat/test-perf-varDS.R b/tests/testthat/test-perf-varDS.R index 9df6c0f6..922db89a 100644 --- a/tests/testthat/test-perf-varDS.R +++ b/tests/testthat/test-perf-varDS.R @@ -26,7 +26,7 @@ set.standard.disclosure.settings() # context("varDS::perf::numeric") test_that("numeric varDS - performance", { - skip_on_cran() +# skip_on_cran() input <- c(0.0, 1.0, 2.0, 3.0, 4.0) @@ -45,10 +45,10 @@ test_that("numeric varDS - performance", { .current.rate <- .count / (difftime(.current.time, .start.time, units = "secs")[[1]]) .reference.rate <- perf.reference.rate("varDS::perf::numeric::0") if (any(length(.reference.rate) == 0) || any(is.null(.reference.rate))) { - print(paste("varDS::perf::numeric::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper())) + write(paste("varDS::perf::numeric::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()), stderr()) perf.reference.save("varDS::perf::numeric::0", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()) } else { - print(paste("varDS::perf::numeric::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = '')) + write(paste("varDS::perf::numeric::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''), stderr()) } .reference.rate <- perf.reference.rate("varDS::perf::numeric::0") @@ -61,7 +61,7 @@ test_that("numeric varDS - performance", { # context("varDS::perf::numeric with NA") test_that("numeric varDS, with NA - performance", { - skip_on_cran() +# skip_on_cran() input <- c(0.0, NA, 2.0, NA, 4.0) @@ -80,10 +80,10 @@ test_that("numeric varDS, with NA - performance", { .current.rate <- .count / (difftime(.current.time, .start.time, units = "secs")[[1]]) .reference.rate <- perf.reference.rate("varDS::perf::numberAndNA::0") if (any(length(.reference.rate) == 0) || any(is.null(.reference.rate))) { - print(paste("varDS::perf::numberAndNA::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper())) + write(paste("varDS::perf::numberAndNA::0 ", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()), stderr()) perf.reference.save("varDS::perf::numberAndNA::0", .current.rate, perf.profile.tolerance.lower(), perf.profile.tolerance.upper()) } else { - print(paste("varDS::perf::numberAndNA::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = '')) + write(paste("varDS::perf::numberAndNA::0 ", format(.current.rate, digits = 8), ", ", format(100.0 * .current.rate / .reference.rate, digits = 4), "%", sep = ''), stderr()) } .reference.rate <- perf.reference.rate("varDS::perf::numberAndNA::0")