Add GCC 14 UBSAN container (Fedora 40)

[pachadotdev]

To address #80 and mimic one of the additional CRAN checks.

[gaborcsardi]

Thanks, we don't need a separate R build for this,if you set -fsanitize=undefined for any recent gcc version, it'll work.

[gaborcsardi]

 => ERROR [14/14] RUN echo -e 'CC = gcc-14 -std=gnu99 -fsanitize=address,undefined -fno-omit-frame-poin  0.5s
------
 > [14/14] RUN echo -e 'CC = gcc-14 -std=gnu99 -fsanitize=address,undefined -fno-omit-frame-pointer\nFC = gfortran-14 -fsanitize=address' >> ~/.R/Makevars:
0.451 /bin/sh: line 1: /root/.R/Makevars: No such file or directory

[gaborcsardi]

Can you please build this image and make sure that it works, i.e. it finds the error in your package, and also in some other packages with gcc-ubsan and gcc-asan errors on CRAN? Thanks!

[pachadotdev]

Can you please build this image and make sure that it works, i.e. it finds the error in your package, and also in some other packages with gcc-ubsan and gcc-asan errors on CRAN? Thanks!

hi @gaborcsardi
I pushed what I had in local (i.e., "gcc" instead of "gcc-14")
Your current image does not support SAN, unless I install libubsan and modify the envvars.
This image does exactly that.

[gaborcsardi]

So can you try to make sure that this image reproduces the errors on CRAN?
https://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-ASAN/iClusterVB/
https://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-ASAN/quantreg/

[gaborcsardi]

Thanks!

[gaborcsardi]

Why is this needed? It is also error prone, because install.packages() does not error on installation failures.

[pachadotdev]

not really needed
the pak part was copied from the gcc14 dockerfile

[gaborcsardi]

Adding this as a global env var is not great, because all programs are going to use it, and the whole system will be very slow.

[pachadotdev]

that was to avoid warnings like "libasan not loaded 1st"

[pachadotdev]

I modified my PR to use the existing image with minimal changes

This is how I can imitate the CRAN setup (https://www.stats.ox.ac.uk/pub/bdr/memtests/README.txt)

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  push:
    branches: [main]
  pull_request:
    branches: [main]

name: R package

permissions: read-all

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}
    container: ${{ matrix.config.container }}

    name: ${{ matrix.config.name }}

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: ubuntu-latest, container: { image: 'ghcr.io/r-hub/containers/gcc13:latest' }, name: 'gcc14'}
          - {os: ubuntu-latest, container: { image: 'your-docker-image:latest' }, name: 'fedora-gcc14'}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes
      ASAN_OPTIONS: 'detect_leaks=0'
      UBSAN_OPTIONS: 'print_stacktrace=1'
      RJAVA_JVM_STACK_WORKAROUND: 0
      RGL_USE_NULL: true
      R_DONT_USE_TK: true
      LD_PRELOAD: /usr/lib64/libasan.so.8

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Set up R environment
        run: |
          mkdir -p ~/.R/
          echo 'CC=gcc -std=gnu11 -fsanitize=address,undefined -fno-omit-frame-pointer' >> ~/.R/Makevars
          echo 'FC=gfortran -fsanitize=address' >> ~/.R/Makevars

      - name: Restore R package cache
        uses: actions/cache@v4
        with:
          path: ~/.cache/R
          key: ${{ runner.os }}-r-${{ matrix.config.r }}-cache

      - name: Install dependencies
        run: |
          Rscript -e 'if (!requireNamespace("pak", quietly = TRUE)) { install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/") }'
          Rscript -e 'pak::pkg_install("decor", dependencies = TRUE)'
          Rscript -e 'pak::pkg_install("rcmdcheck", dependencies = TRUE)'
          Rscript -e 'pak::pkg_install("pkgbuild", dependencies = TRUE)'
          Rscript -e 'pak::pkg_install(".", dependencies = TRUE)'
        working-directory: ./rpkg
        
      - name: Check
        run: |
          Rscript -e 'pkgbuild::check_build_tools(debug = TRUE)'
          Rscript -e 'rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), build_args = "--no-manual", error_on = "error")'
        working-directory: ./rpkg

      - name: Save R package cache
        uses: actions/cache@v4
        with:
          path: ~/.cache/R
          key: ${{ runner.os }}-r-${{ matrix.config.r }}-cache