Vignette restyling

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,143 @@
+on:
+  push:
+  pull_request:
+    branches:
+      - devel
+  schedule:
+    - cron: '0 8 * * 5'
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    container: ${{ matrix.config.image }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.bioc }} - ${{ matrix.config.image }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - { os: windows-latest, bioc: 'devel'}
+        - { os: macOS-latest, bioc: 'devel', curlConfigPath: '/usr/bin/'}
+        - { os: ubuntu-latest, bioc: 'devel'}
+        # - { os: ubuntu-latest, bioc: 'devel', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+        - { os: ubuntu-latest, image: 'bioconductor/bioconductor_docker:devel'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      CRAN: ${{ matrix.config.cran }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CURL_CONFIG: ${{ matrix.config.curlConfigPath }}curl-config
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v2
+
+      - name: Set up R and install BiocManager
+        uses: grimbough/bioc-actions/setup-bioc@v1
+        if: matrix.config.image == null
+        with:
+          bioc-version: ${{ matrix.config.bioc }}
+
+      - name: Set up pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+        if: matrix.config.image == null
+
+      - name: Install remotes
+        run: |
+          install.packages('remotes')
+        shell: Rscript {0}
+
+      - name: Query dependencies
+        run: |
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE, repos = c(getOption('repos'), BiocManager::repositories())), 'depends.Rds', version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows' && matrix.config.image == null
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }}
+          restore-keys: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          pak-version: devel
+
+      - name: Install system dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install --cask xquartz
+          brew install fftw
+
+      # - name: Set up gfortran symlinks (macOS)
+      #   if: runner.os == 'macOS'
+      #   run: |
+      #     set -x
+      #     sudo ln -s /usr/local/Cellar/gcc@11/*/lib/gcc/11 /usr/local/gfortran/lib
+      #     gfortran --version
+
+      - name: Install dependencies
+        run: |
+          local_deps <- remotes::local_package_deps(dependencies = TRUE)
+          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
+          BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 2L)
+          remotes::install_cran('rcmdcheck', Ncpu = 2L)
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Build, Install, Check
+        uses: grimbough/bioc-actions/build-install-check@v1
+
+      # - name: Run BiocCheck
+      #   uses: grimbough/bioc-actions/run-BiocCheck@v1
+      #   with:
+      #     arguments: '--no-check-bioc-views --no-check-bioc-help'
+      #     error-on: 'error'
+
+      # - name: Upload check results
+      #   if: failure()
+      #   uses: actions/upload-artifact@master
+      #   with:
+      #     name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+      #     path: check
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-results
+          path: check
+
+      - name: Test coverage
+        if: matrix.config.os == 'macOS-latest'
+        run: |
+          install.packages("covr")
+          covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")
+        shell: Rscript {0}
+
+      # - name: Deploy
+      #   if: github.event_name == 'push' && github.ref == 'refs/heads/devel' && matrix.config.os == 'macOS-latest'
+      #   run: |
+      #     R CMD INSTALL .
+      #     Rscript -e "remotes::install_dev('pkgdown'); pkgdown::deploy_to_branch(new_process = FALSE)"

DESCRIPTION

@@ -1,27 +1,55 @@
 Package: pathview
 Type: Package
 Title: a tool set for pathway based data integration and visualization
-Version: 1.47.1
-Date: 2025-03-28
-Author: Weijun Luo
-Maintainer: Weijun Luo <luo_weijun@yahoo.com>
-Description: Pathview is a tool set for pathway based data integration
-        and visualization. It maps and renders a wide variety of
-        biological data on relevant pathway graphs. All users need is
-        to supply their data and specify the target pathway. Pathview
-        automatically downloads the pathway graph data, parses the data
-        file, maps user data to the pathway, and render pathway graph
-        with the mapped data. In addition, Pathview also seamlessly
-        integrates with pathway and gene set (enrichment) analysis tools for
-        large-scale and fully automated analysis.
-biocViews: Pathways, GraphAndNetwork, Visualization,
-        GeneSetEnrichment, DifferentialExpression, GeneExpression,
-        Microarray, RNASeq, Genetics, Metabolomics, Proteomics,
-        SystemsBiology, Sequencing
-Depends: R (>= 2.10)
-Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils
-Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics
+Version: 1.47.2
+Date: 2025-12-04
+Authors@R:
+    c(
+        person(
+            given = "Weijun", family = "Luo", role = c("aut", "cre"),
+            email = "luo_weijun@yahoo.com"
+        ),
+        person(
+            given = "Federico", family = "Marini", role = c("ctb"), 
+            email = "marinif@uni-mainz.de", comment = c(ORCID = "0000-0003-3252-7758")
+        )
+    )
+Description: 
+    Pathview is a tool set for pathway based data integration
+    and visualization. It maps and renders a wide variety of
+    biological data on relevant pathway graphs. All users need is
+    to supply their data and specify the target pathway. Pathview
+    automatically downloads the pathway graph data, parses the data
+    file, maps user data to the pathway, and render pathway graph
+    with the mapped data. In addition, Pathview also seamlessly
+    integrates with pathway and gene set (enrichment) analysis tools for
+    large-scale and fully automated analysis.
+biocViews: Pathways, GraphAndNetwork, Visualization, GeneSetEnrichment, 
+    DifferentialExpression, GeneExpression, Microarray, RNASeq, Genetics, 
+    Metabolomics, Proteomics, SystemsBiology, Sequencing
+Depends: 
+    R (>= 2.10)
+Imports: 
+    KEGGgraph, 
+    XML, 
+    Rgraphviz, 
+    graph, 
+    png, 
+    AnnotationDbi, 
+    org.Hs.eg.db, 
+    KEGGREST, 
+    methods, 
+    BiocManager,
+    utils
+Suggests: 
+    knitr,
+    BiocStyle,
+    gage, 
+    org.Mm.eg.db, 
+    RUnit, 
+    BiocGenerics
 License: GPL (>=3.0)
-URL:  https://github.com/datapplab/pathview, https://pathview.uncc.edu/
+VignetteBuilder: knitr
+URL: https://github.com/datapplab/pathview, https://pathview.uncc.edu/
 LazyLoad: yes
-LazyData: yes
+LazyData: yes

NAMESPACE

@@ -11,12 +11,14 @@ importClassesFrom(AnnotationDbi,AnnotationDb)
 importFrom(org.Hs.eg.db, org.Hs.eg.db)
 
 importFrom(png, readPNG)
-importFrom(utils, data, installed.packages, read.delim, globalVariables)
+importFrom(utils, data, installed.packages, read.delim, globalVariables,
+           download.file)
 importFrom(XML, xmlAttrs, xmlChildren, xmlName, xmlRoot, xmlTreeParse)
 importFrom(grDevices, col2rgb, dev.off, pdf, png, rgb)
 importFrom(graphics, image, layout, par, polygon,
            rasterImage, rect, segments, text)
 importFrom(stats, IQR, rnorm)
+importFrom(BiocManager, install)
 
 export(
        download.kegg,
@@ -31,7 +33,7 @@ export(
        sim.mol.data,
 
        node.color, col.key,
-       
+
        wordwrap, strfit,
 
        pathview,