Merge pull request #1021 from OHDSI/develop

Hot fix 3.1.2

.github/workflows/R_CMD_check_Hades.yml

@@ -3,10 +3,11 @@
 on:
   push:
     branches:
-      - '**'
+      - develop
+      - main
   pull_request:
     branches:
-      - '**'
+      - main
 
 name: R-CMD-check
 

.github/workflows/R_CMD_check_Hades_minor.yml

@@ -0,0 +1,128 @@
+#Designed to be a fast github actions check - longer running actions to only run on releases
+on:
+  pull_request:
+    branches:
+      - '**'
+      - '!main'
+
+name: R-CMD-check-minor
+
+jobs:
+  R-CMD-check-minor:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      max-parallel: 1
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}  # Does not appear to have Java 32-bit, hence the --no-multiarch
+          - {os: macOS-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GH_TOKEN }}
+      BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      #CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
+      #CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
+      #CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
+      #CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
+      #CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
+      CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
+      CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
+      CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
+      CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
+      CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
+      #CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
+      #CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
+      #CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
+      #CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
+      #CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
+      #CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
+      #CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
+      #CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
+      #CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
+      #CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-tinytex@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install libssh-dev
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch"))
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Install covr
+        if: runner.os == 'macOS'
+        run: |
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Remove check folder if exists
+        if: runner.os == 'macOS'
+        run: unlink("check", recursive = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--no-multiarch"), build_args = c("--no-manual"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+
+      - name: Upload source package
+        if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
+        uses: actions/upload-artifact@v2
+        with:
+          name: package_tarball
+          path: check/*.tar.gz
+
+      - name: Test coverage
+        if: runner.os == 'macOS'
+        run: covr::codecov()
+        shell: Rscript {0}

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: CohortDiagnostics
 Type: Package
 Title: Diagnostics for OHDSI Cohorts
-Version: 3.1.1
-Date: 2022-07-20
+Version: 3.1.2
+Date: 2022-12-19
 Authors@R: c(
     person("Gowtham", "Rao", email = "[email protected]", role = c("aut", "cre")),
     person("Martijn", "Schuemie", email = "[email protected]", role = c("aut")),

NEWS.md

@@ -1,3 +1,10 @@
+CohortDiagnostics 3.1.2
+=======================
+Bug Fixes:
+
+1. Removed package dependency snapshot capture as it was breaking on newer versions of R
+
+
 CohortDiagnostics 3.1.1
 =======================
 Changes:

R/CohortCharacterizationDiagnostics.R

@@ -48,12 +48,15 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
           covariateSettings = covariateSettings,
           aggregated = TRUE
         )
-    })
+    }
+  )
   populationSize <-
     attr(x = featureExtractionOutput, which = "metaData")$populationSize
   populationSize <-
-    dplyr::tibble(cohortId = names(populationSize) %>% as.numeric(),
-                  populationSize = populationSize)
+    dplyr::tibble(
+      cohortId = names(populationSize) %>% as.numeric(),
+      populationSize = populationSize
+    )
 
   if (!"analysisRef" %in% names(results)) {
     results$analysisRef <- featureExtractionOutput$analysisRef
@@ -82,8 +85,8 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
       dplyr::mutate(p = sumValue / populationSize)
 
     if (nrow(covariates %>%
-               dplyr::filter(p > 1) %>%
-               dplyr::collect()) > 0) {
+      dplyr::filter(p > 1) %>%
+      dplyr::collect()) > 0) {
       stop(
         paste0(
           "During characterization, population size (denominator) was found to be smaller than features Value (numerator).",
@@ -98,37 +101,37 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
       dplyr::rename(mean = averageValue) %>%
       dplyr::select(-populationSize)
 
-      if (FeatureExtraction::isTemporalCovariateData(featureExtractionOutput)) {
-        covariates <- covariates %>%
-          dplyr::select(
-            cohortId,
-            timeId,
-            covariateId,
-            sumValue,
-            mean,
-            sd
-          )
-          if (length(is.na(covariates$timeId)) > 0) {
-            covariates[is.na(covariates$timeId),]$timeId <- -1
-          }
-      } else {
-        covariates <- covariates %>%
-          dplyr::mutate(timeId = 0) %>%
-          dplyr::select(
-            cohortId,
-            timeId,
-            covariateId,
-            sumValue,
-            mean,
-            sd
-          )
-      }
-      if ("covariates" %in% names(results)) {
-        Andromeda::appendToTable(results$covariates, covariates)
-      } else {
-        results$covariates <- covariates
+    if (FeatureExtraction::isTemporalCovariateData(featureExtractionOutput)) {
+      covariates <- covariates %>%
+        dplyr::select(
+          cohortId,
+          timeId,
+          covariateId,
+          sumValue,
+          mean,
+          sd
+        )
+      if (length(is.na(covariates$timeId)) > 0) {
+        covariates[is.na(covariates$timeId), ]$timeId <- -1
       }
+    } else {
+      covariates <- covariates %>%
+        dplyr::mutate(timeId = 0) %>%
+        dplyr::select(
+          cohortId,
+          timeId,
+          covariateId,
+          sumValue,
+          mean,
+          sd
+        )
     }
+    if ("covariates" %in% names(results)) {
+      Andromeda::appendToTable(results$covariates, covariates)
+    } else {
+      results$covariates <- covariates
+    }
+  }
 
   if ("covariatesContinuous" %in% names(featureExtractionOutput) &&
     dplyr::pull(dplyr::count(featureExtractionOutput$covariatesContinuous)) > 0) {
@@ -151,12 +154,14 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
           sd
         )
       if (length(is.na(covariates$timeId)) > 0) {
-        covariates[is.na(covariates$timeId),]$timeId <- -1
+        covariates[is.na(covariates$timeId), ]$timeId <- -1
       }
     } else {
       covariates <- covariates %>%
-        dplyr::mutate(sumValue = -1,
-                      timeId = 0) %>%
+        dplyr::mutate(
+          sumValue = -1,
+          timeId = 0
+        ) %>%
         dplyr::select(
           cohortId,
           timeId,
@@ -179,10 +184,12 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
   }
 
   delta <- Sys.time() - startTime
-  ParallelLogger::logInfo("Cohort characterization took ",
-                          signif(delta, 3),
-                          " ",
-                          attr(delta, "units"))
+  ParallelLogger::logInfo(
+    "Cohort characterization took ",
+    signif(delta, 3),
+    " ",
+    attr(delta, "units")
+  )
   return(results)
 }
 
@@ -221,9 +228,10 @@ executeCohortCharacterization <- function(connection,
   )
 
   if (!incremental) {
-    for (outputFile in c(covariateValueFileName, covariateValueContFileName,
-                         covariateRefFileName, analysisRefFileName, timeRefFileName)) {
-
+    for (outputFile in c(
+      covariateValueFileName, covariateValueContFileName,
+      covariateRefFileName, analysisRefFileName, timeRefFileName
+    )) {
       if (file.exists(outputFile)) {
         ParallelLogger::logInfo("Not in incremental mode - Removing file", outputFile, " and replacing")
         unlink(outputFile)
@@ -309,10 +317,12 @@ executeCohortCharacterization <- function(connection,
     }
   }
   delta <- Sys.time() - startCohortCharacterization
-  ParallelLogger::logInfo("Running ",
-                          jobName,
-                          " took",
-                          signif(delta, 3),
-                          " ",
-                          attr(delta, "units"))
+  ParallelLogger::logInfo(
+    "Running ",
+    jobName,
+    " took",
+    signif(delta, 3),
+    " ",
+    attr(delta, "units")
+  )
 }