Merge branch 'main' of github.com:ratschlab/ricu into merge-yaib-configs

.github/workflows/check.yaml

@@ -6,55 +6,55 @@ on:
     branches:
       - main
 
-name: check
-
 jobs:
-  check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+  R-CMD-check:
+    name: R CMD check (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        config:
-          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,  r: 'release'}
-          - {os: ubuntu-latest,  r: 'oldrel-1'}
-
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_KEEP_PKG_SOURCE: yes
+         os: ['ubuntu-latest']
 
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-tinytex@v2
-      - run: tlmgr --version
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: actions/checkout@v4
+      - name: Set up Conda env
+        uses: mamba-org/provision-with-micromamba@e2b397b12d0a38069451664382b769c9456e3d6d
         with:
-          extra-packages: |
-            any::rcmdcheck
-            eth-mds/mimic-demo
-            eth-mds/eicu-demo
-            nbenn/mockthat
-
-      - uses: r-lib/actions/check-r-package@v2
+          cache-env: true
+      - name: Install TinyTex
+        shell: bash -l {0}
+        run: |
+          Rscript -e 'tinytex::install_tinytex()'
+      - name: Install demo datasets
+        shell: bash -l {0}
+        run: |
+          Rscript -e 'install.packages("eicu.demo", repos="https://eth-mds.github.io/physionet-demo")'
+      - name: Run R CMD check
+        shell: bash -l {0}
+        run: |
+          R CMD build . && R CMD check --no-manual --as-cran $(ls -t . | head -n1)
         env:
           _R_CHECK_CRAN_INCOMING_: false
           _R_CHECK_FORCE_SUGGESTS_: false
-          _R_CHECK_DOC_SIZES_: false
-        with:
-          upload-snapshots: true
+      # R CMD check raises a warning by qpdf that the generated docs PDF is large and
+      # should be compressed. Currently we ignore this warning via the grep below.
+      - name: Check for warnings
+        shell: bash -l {0}
+        run: |
+          CHECK_LOG_FILE=ricu.Rcheck/00check.log
+          CHECK_INSTALL_FILE=ricu.Rcheck/00install.out
+          if ! [[ -f "$CHECK_LOG_FILE" ]]; then
+            echo "Log-file not found."
+            exit 1
+          fi
+          if cat $CHECK_LOG_FILE | grep -q "ERROR"; then
+            cat $CHECK_INSTALL_FILE
+            cat $CHECK_LOG_FILE
+            exit 1
+          fi
+          if cat $CHECK_LOG_FILE | grep -q "WARNING" | grep -q -v -e "checking sizes of PDF files under ‘inst/doc’ ... WARNING"; then
+            echo "Found warnings, treated as errors."
+            cat $CHECK_LOG_FILE
+            exit 1
+          fi

DESCRIPTION

@@ -70,7 +70,7 @@ Suggests:
     pdftools,
     magick,
     pillar
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Additional_repositories: https://eth-mds.github.io/physionet-demo
 VignetteBuilder: knitr
 Config/testthat/edition: 3

NAMESPACE

@@ -92,12 +92,14 @@ S3method(do_callback,fun_itm)
 S3method(do_callback,hrd_itm)
 S3method(do_callback,itm)
 S3method(do_callback,rec_cncpt)
+S3method(do_callback,sic_itm)
 S3method(do_itm_load,col_itm)
 S3method(do_itm_load,default)
 S3method(do_itm_load,fun_itm)
 S3method(do_itm_load,hrd_itm)
 S3method(do_itm_load,itm)
 S3method(do_itm_load,nul_itm)
+S3method(do_itm_load,sic_itm)
 S3method(downgrade_id,default)
 S3method(downgrade_id,id_tbl)
 S3method(downgrade_id,ts_tbl)
@@ -126,6 +128,7 @@ S3method(id_map_helper,default)
 S3method(id_map_helper,src_env)
 S3method(id_orig_helper,default)
 S3method(id_orig_helper,miiv_env)
+S3method(id_orig_helper,sic_env)
 S3method(id_orig_helper,src_env)
 S3method(id_vars,col_cfg)
 S3method(id_vars,default)
@@ -139,6 +142,7 @@ S3method(id_win_helper,eicu_env)
 S3method(id_win_helper,hirid_env)
 S3method(id_win_helper,miiv_env)
 S3method(id_win_helper,mimic_env)
+S3method(id_win_helper,picdb_env)
 S3method(id_win_helper,sic_env)
 S3method(import_src,aumc_cfg)
 S3method(import_src,character)
@@ -164,6 +168,7 @@ S3method(init_itm,hrd_itm)
 S3method(init_itm,itm)
 S3method(init_itm,rgx_itm)
 S3method(init_itm,sel_itm)
+S3method(init_itm,sic_itm)
 S3method(interval,default)
 S3method(interval,difftime)
 S3method(interval,itm)
@@ -188,6 +193,7 @@ S3method(load_difftime,eicu_tbl)
 S3method(load_difftime,hirid_tbl)
 S3method(load_difftime,miiv_tbl)
 S3method(load_difftime,mimic_tbl)
+S3method(load_difftime,picdb_tbl)
 S3method(load_difftime,sic_tbl)
 S3method(load_id,character)
 S3method(load_id,default)
@@ -232,6 +238,7 @@ S3method(prepare_query,default)
 S3method(prepare_query,hrd_itm)
 S3method(prepare_query,rgx_itm)
 S3method(prepare_query,sel_itm)
+S3method(prepare_query,sic_itm)
 S3method(print,cncpt)
 S3method(print,id_tbl)
 S3method(print,itm)

R/data-env.R

@@ -239,6 +239,10 @@ NULL
 #' @rdname data_env
 NULL
 
+#' @name picdb
+#' @rdname data_env
+NULL
+
 data_env <- function() get("data", envir = pkg_env(), mode = "environment")
 
 #' Data source environments

test_environment.yaml → environment.yml

@@ -1,4 +1,4 @@
-name: ricu-test
+name: ricu
 channels:
   - nodefaults
   - conda-forge
@@ -18,7 +18,6 @@ dependencies:
   - r-cli>=2.1.0
   - r-fansi
   - r-openssl
-  - r-units
   # optional
   - r-rticles
   - r-forestmodel
@@ -29,4 +28,13 @@ dependencies:
   - r-cowplot
   - r-knitr
   - r-pdftools
-  - r-covr
+  - r-covr
+  - r-units
+  - r-tinytex
+  - r-testthat
+  - r-mockthat
+  - r-pkgload
+  - r-codetools
+  - r-qpdf
+  - qpdf
+  - r-mimic.demo