run as fast as you can to stay in the same place

.Rbuildignore

@@ -1,6 +1,11 @@
+examples
+repo
 revdep
+scripts
 tools
-examples
+wiki
+www
+yaml
 tests/Makefile
 tests/(.+?)\.png$
 tests/(.+?)\.pdf$
@@ -34,13 +39,10 @@ TODO\.md$
 \.tests
 Makefile
 rules.mk
-yaml
-scripts
 lib
 libs
 library
 check
-www
 ^(.+?)\.pdf
 ^(.+?)\.tar\.gz
 ^(.+?)\.tgz

.github/workflows/binary-build.yml

@@ -5,13 +5,43 @@ on:
     tags:
       - '**'
   workflow_dispatch:
-    branches:
-      - '*'
 
 name: binary-build
 
+env:
+  release_name: ${{ vars.repo_name }}_${{ github.ref_name }}
+
 jobs:
-  binary-build:
+  source_build:          
+    runs-on: ubuntu-latest
+    name: Build source tarball
+    strategy:
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: latest
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::pkgbuild
+
+      - name: Build source tarball
+        run: |
+          R CMD build --force --no-manual --resave-data --compact-vignettes=both --md5 .
+          mkdir -p ${{ github.workspace }}/artifacts
+          cp ${{ env.release_name }}.tar.gz ${{ github.workspace }}/artifacts
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: source_tarball
+          path: ${{ github.workspace }}/artifacts/${{ env.release_name }}.tar.gz
+
+  binary_build:
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -20,37 +50,47 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-latest,  r: 'release'}
-          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_KEEP_PKG_SOURCE: yes
+          - {os: macOS-latest,   r: 'release', ext: "tgz"}
+          - {os: windows-latest, r: 'release', ext: "zip"}
 
     steps:
-      - uses: actions/checkout@v3.1.0
+      - uses: actions/checkout@v4
 
       - 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
         with:
-          extra-packages: rcmdcheck 
-
+          extra-packages: |
+            any::pkgbuild
+
       - name: Build binary
         run: pkgbuild::build(binary=TRUE,manual=TRUE)
         shell: Rscript {0}
-      
-      - name: Copying tarball
+
+      - name: Copy tarball
         run: |
           mkdir -p ${{ github.workspace }}/artifacts
-          cp ../tao_* ${{ github.workspace }}/artifacts
-          
-      - uses: actions/upload-artifact@v3.1.1
+          cp ../${{ env.release_name }}.${{ matrix.config.ext }} ${{ github.workspace }}/artifacts
+
+      - uses: actions/upload-artifact@v4
         with:
-          name: binary-${{ matrix.config.os }}-${{ matrix.config.r }}
-          path: ${{ github.workspace }}/artifacts
+          name: ${{ matrix.config.os }}-${{ matrix.config.r }}
+          path: ${{ github.workspace }}/artifacts/${{ env.release_name }}.${{ matrix.config.ext }}
+
+# Workflow derived from https://github.com/marketplace/actions/create-release
+  create_release:
+    needs: [ source_build, binary_build ]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/download-artifact@v4
+      with:
+        path: artifacts
+    - uses: ncipollo/release-action@v1
+      with:
+        draft: true
+        artifacts: "artifacts/*/*"

.github/workflows/r-cmd-check.yml

@@ -4,11 +4,24 @@ on:
   push:
     branches:
       - '*'
+    paths:
+      - DESCRIPTION
+      - NAMESPACE
+      - R/**
+      - src/**
+      - tests/**
+      - man/**
+      - data/**
   pull_request:
-    branches: [master]
+    paths:
+      - DESCRIPTION
+      - NAMESPACE
+      - R/**
+      - src/**
+      - tests/**
+      - man/**
+      - data/**
   workflow_dispatch:
-    branches:
-      - '*'
 
 name: R-CMD-check
 
@@ -22,56 +35,34 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-22.04,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,  r: 'release'}
-          - {os: ubuntu-latest,  r: 'oldrel-1'}
-          - {os: ubuntu-20.04,   r: '4.0.0'}
-          - {os: macOS-11,       r: 'release'}
-          - {os: macOS-12,       r: 'release'}
+          - {os: ubuntu-20.04,   r: '4.1.0'}
+          - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-      _R_CHECK_DEPENDS_ONLY_: false
-      _R_CHECK_ALL_NON_ISO_C_: true
-      _R_CHECK_CODE_ASSIGN_TO_GLOBALENV_: true
-      _R_CHECK_CODE_ATTACH_: true
-      _R_CHECK_CODE_DATA_INTO_GLOBALENV_: true
-      _R_CHECK_CODE_USAGE_VIA_NAMESPACES_: true
-      _R_CHECK_DEPRECATED_DEFUNCT_: true
-      _R_CHECK_EXECUTABLES_EXCLUSIONS_: false
-      _R_CHECK_INSTALL_DEPENDS_: true
-      _R_CHECK_NO_RECOMMENDED_: true
-      _R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_: true
-      _R_CHECK_REPLACING_IMPORTS_: true
-      _R_CHECK_S3_METHODS_NOT_REGISTERED_: true
-      _R_CHECK_SCREEN_DEVICE_: stop
-      _R_CHECK_SRC_MINUS_W_IMPLICIT_: true
-      _R_CHECK_SRC_MINUS_W_UNUSED_: true
-      _R_CHECK_SUGGESTS_ONLY_: true
-      _R_CHECK_TOPLEVEL_FILES_: true
-      _R_CHECK_VC_DIRS_: true
-      _R_CHECK_WALL_FORTRAN_: true
-      _R_CHECK_USE_CODETOOLS_: true
-      _R_CHECK_CODETOOLS_PROFILE_: "suppressLocalUnused=FALSE,suppressPartialMatchArgs=FALSE,suppressParamUnused=TRUE,suppressUndefined=FALSE"
 
     steps:
-      - uses: actions/checkout@v3.1.0
+      - uses: actions/checkout@v4
 
       - 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
+          extra-repositories: |
+            https://kingaa.github.io/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
 
       - uses: r-lib/actions/check-r-package@v2
 
-      - uses: actions/upload-artifact@v3.1.1
+      - uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.config.os }}-${{ matrix.config.r }}-results
-          path: check
+          path: check/${{ vars.repo_name }}.Rcheck/00check.log

.github/workflows/test-coverage.yml

@@ -1,13 +1,27 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/master/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
+  workflow_dispatch:
   push:
     branches: [master]
+    paths:
+      - DESCRIPTION
+      - NAMESPACE
+      - R/**
+      - src/**
+      - tests/**
+      - man/**
+      - data/**
   pull_request:
     branches: [master]
-  workflow_dispatch:
-    branches:
-      - '*'
+    paths:
+      - DESCRIPTION
+      - NAMESPACE
+      - R/**
+      - src/**
+      - tests/**
+      - man/**
+      - data/**
 
 name: test-coverage
 
@@ -18,7 +32,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3.1.0
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

.gitignore

@@ -17,15 +17,14 @@
 *.so
 *.gcda
 *.gcno
-tests/*.pdf
-scripts
+*.pdf
 lib
 library
 check
+repo
+wiki
 www
-*.pdf
-inst/doc/figure
-inst/doc/cache
+tmp
 covr.html
 covr.rds
 .DS_Store

BUILD.md

@@ -0,0 +1,68 @@
+----------------
+
+# Instructions for building, checking, and installing
+
+## Makefile usage
+
+A `Makefile` is provided.  Most of the rules are defined in the `rules.mk` file.
+The following key variables are defined in the `Makefile`.
+
+- `REPODIR`: the name of the directory in which a local copy of the Git repo used for publishing source and documentation is located.
+- `INCLUDES`: names of header files that will be copied to `inst/includes`
+- `HEADERS`: names of header files that must be rebuilt whenever source code changes.
+
+The key targets are:
+
+- `roxy`: runs `devtools::document()` to build the help pages (in `man/`), the package `NAMESPACE`, and the collation order in `DESCRIPTION`.
+- `dist`: builds the package source tarball.
+- `install`: installs the package locally for testing.
+- `tests`: runs `make` in the `tests/` directory, causing tests to be updated as needed.
+- `clean`: cleans the directory of files created during builds and tests.
+- `fresh`: resets the directory for a fresh rebuild.
+
+- `htmlhelp`: builds the package manual in HTML and PDF formats.
+  This command also causes `doxygen` to be run, which produces HTML documentation of the C/C++ source code.
+  These documentation files are installed into the `REPODIR/manuals` directory.
+- `www`: installs the package and runs `make` in the `www` directory.
+  This causes vignettes to be updated, among other things.
+- `NEWS`: builds the plain-text package NEWS file.
+- `instdocs`: runs `make` in the `inst/docs` directory.
+
+- `check`: runs `devtools::check()`.
+- `qcheck`: like `check`, but tests in `tests/` are not run.
+- `qqcheck`: like `qcheck`, but checks for code-documentation mismatch and examples are not run.
+- `xcheck`: runs `devtools::check(cran=TRUE)`, i.e., the additional checks for CRAN suitability are also run.
+- `ycheck`: runs `xcheck` but tests and examples that are ordinarily not run (because expensive) are run.
+- `vcheck`: runs `check` and then tests for memory leaks using `valgrind`.
+  One must examine the output (printed to the console and also stored in a file, the name of which ends in `-Ex.Rout`.
+- `revdeps`: causes checks of reverse-dependent packages to run.
+  The outputs are stored under the `revdep` directory.
+- `rchk`: runs Kalibera's `rchk` utility.
+  This uses `docker` to download and run a Docker container.
+  The stdout for this is stored in `rchk.out`.
+
+- `session`: installs the package locally and then runs an **R** session for interactive testing.
+  This session is controlled by the `RSESSION` environment variable.
+  By default, this runs an `emacs -f R` session.
+- `rsession`: like `session`, but a naked **R** session is started: `RSESSION=R`.
+- `debug`: like `rsession`, but the **R** session is started under a debugger.
+  By default, the `gdb` debugger is used: `RSESSION=R -d gdb`.
+
+- `publish`: causes source and binary tarballs to be installed in the REPODIR respository.
+- `covr`: runs `covr::package_coverage()` to evaluate unit-test coverage.
+  Results are stored in `covr.rds`.
+- `vcovr`: like `covr`, but results are displayed in a browser. 
+
+----------------
+
+## Github Actions
+
+Several Github Actions are defined in `.github/workflows`:
+
+- `r-cmd-check`: runs checks on various platforms.
+- `test-coverage`: runs `covr::codecov` to upload unit-test coverage information to [codecov.io](https://codecov.io).
+- `binary-build`: causes binary tarballs to be built for OS X and Windows platforms.
+
+These must be updated manually from time to time as the Actions on which they depend change.
+
+----------------

DESCRIPTION

@@ -10,4 +10,4 @@ License: GPL-3
 Encoding: UTF-8
 Suggests: tinytest
 Roxygen: list(roclets = c("collate", "namespace", "rd", "roxytest::tinytest_roclet"))
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

Makefile

@@ -1,6 +1,6 @@
-REPODIR = ../www
-INCLUDES=
-HEADERS=
+REPODIR = repo
+INCLUDES =
+HEADERS =
+SESSION_PKGS = datasets,utils,grDevices,graphics,stats,methods,tidyverse,$(PKG)
 
 include rules.mk
-