Merge branch 'develop'

OHDSI · Oct 30, 2023 · 4d89788 · 4d89788
2 parents 2b8eb20 + 6141974
commit 4d89788
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Showing 46 changed files with 838 additions and 189 deletions.
diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml
@@ -20,12 +20,12 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}  # Does not appear to have Java 32-bit, hence the --no-multiarch
+          - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-#          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
+      GITHUB_PAT: ${{ secrets.GH_TOKEN }}
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
@@ -43,75 +43,51 @@ jobs:
       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 }}
+      CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
+      CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
+      CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
+      WEBAPI_TEST_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_WEBAPI_URL }}
+      WEBAPI_TEST_SECURE_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_SECURE_WEBAPI_URL }}
+      WEBAPI_TEST_ADMIN_USER_NAME: ${{ secrets.WEBAPI_TEST_ADMIN_USER_NAME }}
+      WEBAPI_TEST_ADMIN_USER_PASSWORD: ${{ secrets.WEBAPI_TEST_ADMIN_USER_PASSWORD }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-tinytex@v1
+      - uses: r-lib/actions/setup-tinytex@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - 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
+      - name: Install system requirements
         if: runner.os == 'Linux'
         run: |
+          sudo apt-get install -y libssh-dev
+          Rscript -e 'install.packages("remotes")'
           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", "--as-cran", "--no-multiarch"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@v2
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          args: 'c("--no-manual", "--as-cran")'
+          build_args: 'c("--compact-vignettes=both")'
+          error-on: '"warning"'
+          check-dir: '"check"'
 
       - name: Upload source package
         if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
@@ -120,6 +96,12 @@ jobs:
           name: package_tarball
           path: check/*.tar.gz
 
+      - name: Install covr
+        if: runner.os == 'macOS'
+        run: |
+          install.packages("covr")
+        shell: Rscript {0}
+
       - name: Test coverage
         if: runner.os == 'macOS'
         run: covr::codecov()
@@ -137,7 +119,7 @@ jobs:
 
     steps:
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
@@ -163,7 +145,7 @@ jobs:
           draft: false
           prerelease: false
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         if: ${{ env.new_version != '' }}
 
       - name: Install drat
@@ -192,3 +174,4 @@ jobs:
         if: ${{ env.new_version != '' }}
         run: |
           curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/
+
diff --git a/Cyclops.Rproj b/Cyclops.Rproj
@@ -1,7 +1,7 @@
 Version: 1.0
 
-RestoreWorkspace: Default
-SaveWorkspace: Default
+RestoreWorkspace: No
+SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: Cyclops
 Type: Package
 Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis
-Version: 3.3.1
+Version: 3.3.1.999
 Authors@R: c(
     person("Marc A.", "Suchard", email = "[email protected]", role = c("aut","cre")),
     person("Martijn J.", "Schuemie", role = "aut"),
@@ -30,7 +30,7 @@ Biarch: true
 URL: https://github.com/ohdsi/cyclops
 BugReports: https://github.com/ohdsi/cyclops/issues
 Depends:
-    R (>= 3.1.0)
+    R (>= 3.5.0)
 Imports:
     rlang,
     Matrix,
@@ -41,7 +41,6 @@ Imports:
     survival,
     bit64
 LinkingTo: Rcpp,
-    BH (>= 1.51.0),
     RcppEigen (>= 0.3.2)
 Suggests:
     testthat,

diff --git a/NAMESPACE b/NAMESPACE
@@ -13,13 +13,15 @@ S3method(survfit,cyclopsFit)
 S3method(vcov,cyclopsFit)
 export(Multitype)
 export(convertToCyclopsData)
+export(convertToTimeVaryingCoef)
 export(coverage)
 export(createAutoGridCrossValidationControl)
 export(createControl)
 export(createCyclopsData)
 export(createNonSeparablePrior)
 export(createParameterizedPrior)
 export(createPrior)
+export(createWeightBasedSearchControl)
 export(finalizeSqlCyclopsData)
 export(fitCyclopsModel)
 export(fitCyclopsSimulation)
@@ -39,6 +41,7 @@ export(meanLinearPredictor)
 export(mse)
 export(readCyclopsData)
 export(simulateCyclopsData)
+export(splitTime)
 import(Matrix)
 import(Rcpp)
 import(dplyr)
@@ -71,5 +74,6 @@ importFrom(stats,terms)
 importFrom(stats,time)
 importFrom(stats,vcov)
 importFrom(survival,Surv)
+importFrom(survival,survSplit)
 importFrom(survival,survfit)
 useDynLib(Cyclops, .registration = TRUE)
diff --git a/NEWS.md b/NEWS.md
@@ -1,23 +1,42 @@
+Cyclops v3.4.0
+==============
+
+Changes:
+
+1. remove dependence on `BH`
+2. improvements on adaptive likelihood profiling
+3. add `auto` option to `cvRepetitions`
+4. bumped explicit C++11 requirement up to R v4.1
+5. removed deprecated use of `dbplyr:::$.tbl_lazy`
+   a. breaking change in `dbplyr v2.4.0`
+
 Cyclops v3.3.1
 ==============
 
 Changes:
 
-1. fix uninitialized value in detected in computeAsymptoticPrecisionMatrix(); value was priorType
-2. fix memory leak caused by call to ::Rf_error()
+1. fix uninitialized value in detected in `computeAsymptoticPrecisionMatrix()`; value was priorType
+2. fix memory leak caused by call to `::Rf_error()`
 3. fix line-endings on Makevar on windows
 
 Cyclops v3.3.0
 ==============
 
-Changes:
-
 1. bump for R 4.2
 2. fix CRAN warnings
     a. used `minValues`
 3. fix CRAN notes
     a. remove explicit dependence on C++11 (except for R <= 4.0)   
 
+Cyclops v3.2.1
+==============
+
+Changes:
+
+1. fix small memory leak caused by direct call to '::Rf_error()'
+2. disable JVM calls on CRAN due to uninitialized memory in Java JVM
+
+
 Cyclops v3.2.0
 ==============
 

diff --git a/R/Cyclops-package.R b/R/Cyclops-package.R
@@ -0,0 +1,6 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL
diff --git a/R/DataManagement.R b/R/DataManagement.R
@@ -634,8 +634,8 @@ reduce <- function(object, covariates, groupBy, power = 1) {
 #' \code{appendSqlCyclopsData} appends data to an OHDSI data object.
 #'
 #' @details Append data using two tables.  The outcomes table is dense and contains ...  The covariates table is sparse and contains ...
-#' All entries in the outcome table must be sorted in increasing order by {oStratumId, oRowId}.  All entries in the covariate table
-#' must be sorted in increasing order by {cRowId}. Each cRowId value must match exactly one oRowId value.
+#' All entries in the outcome table must be sorted in increasing order by (oStratumId, oRowId).  All entries in the covariate table
+#' must be sorted in increasing order by (cRowId). Each cRowId value must match exactly one oRowId value.
 #'
 #' @param object    OHDSI Cyclops data object to append entries
 #' @param oStratumId    Integer vector (optional): non-unique stratum identifier for each row in outcomes table