r-hub · gaborcsardi · Feb 4, 2025 · Feb 4, 2025
diff --git a/builder/Dockerfile.fedora-gcc15 b/builder/Dockerfile.fedora-gcc15
@@ -0,0 +1,89 @@
+
+FROM fedora:42
+
+ENV OS_IDENTIFIER fedora-42
+
+RUN dnf -y upgrade \
+    && dnf -y install dnf-plugins-core \
+    && dnf -y install \
+    autoconf \
+    automake \
+    bzip2-devel \
+    cairo-devel \
+    gcc \
+    g++ \
+    gfortran \
+    java-21-openjdk-devel \
+    libICE-devel \
+    libSM-devel \
+    libX11-devel \
+    libXmu-devel \
+    libXt-devel \
+    libcurl-devel \
+    libicu-devel \
+    libjpeg-devel \
+    libpng-devel \
+    libtiff-devel \
+    libtool \
+    make \
+    ncurses-devel \
+    pango-devel \
+    pcre-devel \
+    pcre2-devel \
+    readline-devel \
+    rpm-build \
+    tcl-devel \
+    tex \
+    texinfo-tex \
+    texlive-collection-latexrecommended \
+    tk-devel \
+    unzip \
+    valgrind-devel \
+    which \
+    wget \
+    xz-devel \
+    zlib-devel \
+    && dnf clean all
+
+RUN if [ "$(arch)" == "aarch64" ]; then echo arm64; else echo amd64; fi > /tmp/arch
+
+RUN curl -LO "https://github.com/goreleaser/nfpm/releases/download/v2.18.1/nfpm_$(cat /tmp/arch).rpm" && \
+    dnf install -y "nfpm_$(cat /tmp/arch).rpm" && \
+    rm "nfpm_$(cat /tmp/arch).rpm"
+
+RUN chmod 0777 /opt
+
+# Configure flags for RHEL 9 that don't use the defaults in build.sh
+ENV CONFIGURE_OPTIONS="\
+    --enable-R-shlib \
+    --with-tcltk \
+    --enable-memory-profiling \
+    --with-x \
+    --with-system-valgrind-headers \
+    --with-tcl-config=/usr/lib64/tclConfig.sh \
+    --with-tk-config=/usr/lib64/tkConfig.sh \
+    --enable-prebuilt-html"
+
+# RHEL 9 doesn't have the inconsolata font, so override the defaults.
+# This may be removed if RHEL ever adds the texlive-inconsolata package from Fedora.
+# Or check `dnf provides '*/inconsolata.sty'` for a package that provides it.
+# https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Making-the-manuals
+ENV R_RD4PDF="times,hyper"
+
+# Make sure that patching Java does not break R.
+# R's default JAVA_HOME path includes the exact Java version on CentOS/RHEL, which
+# requires users to run `R CMD javareconf` even on minor/patch upgrades. Use the
+# major version symlink to avoid this.
+# https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
+# https://solutions.posit.co/envs-pkgs/using-rjava/
+ENV JAVA_HOME=/usr/lib/jvm/jre-11-openjdk
+
+# R 3.x requires PCRE2 for Pango support on RHEL 9
+ENV INCLUDE_PCRE2_IN_R_3 yes
+
+COPY builder/config.fedora-gcc /config.site
+COPY builder/config.fedora-gcc.aarch64 /config.site.aarch64
+
+COPY builder/package.fedora-gcc /package.sh
+COPY build.sh .
+ENTRYPOINT ./build.sh
diff --git a/containers/gcc15/Dockerfile b/containers/gcc15/Dockerfile
@@ -0,0 +1,120 @@
+
+FROM fedora:42
+
+# ------------------------------------------------------------------------------------
+# Install pre-built R and requirements
+
+RUN dnf -y upgrade && \
+    dnf -y install dnf-plugins-core && \
+    dnf -y install curl && \
+    curl -LO "https://github.com/r-hub/containers/releases/download/latest/R-rstudio-fedora-40-devel-gcc15-1-1.$(arch).rpm" && \
+    yum install -y R-*.rpm && \
+    rm R-*.rpm
+
+# Extra system packages that pak does not know about
+RUN dnf install -y flexiblas
+RUN dnf install -y https://rpms.r-pkg.org/fedora-38/jags-4.3.2-1.$(arch).rpm
+
+# ------------------------------------------------------------------------------------
+# Put R on PATH
+# AUto-install system requirements
+
+ENV PATH="/opt/R/devel-gcc15/bin:${PATH}"
+ENV PKG_SYSREQS=true
+ENV R_PKG_SYSREQS2=true
+
+# ------------------------------------------------------------------------------------
+# Set CRAN repo, no P3M for Fedora
+
+RUN echo 'options(repos =c(CRAN = "https://cran.rstudio.com"))' \
+    >> /opt/R/devel-gcc15/lib/R/library/base/R/Rprofile
+
+RUN if [ "$(arch)" = "x86_64" ]; then \
+        . /etc/os-release; \
+        RVER=$(R -s -e 'cat(paste(getRversion()[,1:2]))'); \
+        echo "options(repos = c(RHUB = 'https://raw.githubusercontent.com/r-hub/repos/main/${ID}-${VERSION_ID}/${RVER}', getOption('repos')))" \
+            >> /opt/R/devel-gcc15/lib/R/library/base/R/Rprofile; \
+        echo 'options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"])))' \
+            >> /opt/R/devel-gcc15/lib/R/library/base/R/Rprofile; \
+    fi
+
+# ------------------------------------------------------------------------------------
+# Install pak
+
+RUN /opt/R/devel-gcc15/bin/R -q -e \
+    'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/%s/%s/%s/%s", "devel", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
+
+# ------------------------------------------------------------------------------------
+# Locale
+
+RUN dnf install -y glibc-langpack-en
+
+ENV LC_ALL en_GB.UTF-8
+ENV LANG en_GB.UTF-8
+
+# ------------------------------------------------------------------------------------
+# Use user's package library for the rest
+
+RUN /opt/R/devel-gcc15/bin/R -q -e 'dir.create(Sys.getenv("R_LIBS_USER"), showWarnings = FALSE, recursive = TRUE)'
+
+# ------------------------------------------------------------------------------------
+# Copy check script
+
+COPY r-check /usr/local/bin
+
+# ------------------------------------------------------------------------------------
+# Useful system packages
+
+RUN dnf -y install pkg-config devscripts-checkbashisms qpdf git tidy
+
+# ------------------------------------------------------------------------------------
+# CRAN's config from https://www.stats.ox.ac.uk/pub/bdr/gcc14/README.txt
+
+ENV _R_CHECK_INSTALL_DEPENDS_ true
+## the next is the default, but --as-cran has true
+ENV _R_CHECK_SUGGESTS_ONLY_ false
+ENV _R_CHECK_NO_RECOMMENDED_ true
+ENV _R_CHECK_DOC_SIZES2_ true
+ENV _R_CHECK_DEPRECATED_DEFUNCT_ true
+ENV _R_CHECK_SCREEN_DEVICE_ warn
+ENV _R_CHECK_REPLACING_IMPORTS_ true
+ENV _R_CHECK_TOPLEVEL_FILES_ true
+ENV _R_CHECK_DOT_FIRSTLIB_ true
+ENV _R_CHECK_RD_LINE_WIDTHS_ true
+ENV _R_CHECK_S3_METHODS_NOT_REGISTERED_ true
+ENV _R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_ true
+ENV _R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_ TRUE
+ENV _R_CHECK_NATIVE_ROUTINE_REGISTRATION_ true
+ENV _R_CHECK_FF_CALLS_ registration
+ENV _R_CHECK_PRAGMAS_ true
+ENV _R_CHECK_COMPILATION_FLAGS_ true
+ENV _R_CHECK_R_DEPENDS_ true
+ENV _R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_ true
+ENV _R_CHECK_PKG_SIZES_ false
+ENV _R_CHECK_SHLIB_OPENMP_FLAGS_ true
+
+ENV _R_CHECK_LIMIT_CORES_ true
+ENV _R_CHECK_LENGTH_1_CONDITION_ package:_R_CHECK_PACKAGE_NAME_,verbose
+#ENV _R_CHECK_LENGTH_1_LOGIC2_="package:_R_CHECK_PACKAGE_NAME_,verbose"
+ENV _R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_ true
+ENV _R_CHECK_COMPILATION_FLAGS_KNOWN_="-Wno-deprecated-declarations -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -Werror=implicit-function-declaration"
+ENV _R_CHECK_AUTOCONF_ true
+ENV _R_CHECK_THINGS_IN_CHECK_DIR_ true
+ENV _R_CHECK_THINGS_IN_TEMP_DIR_ true
+ENV _R_CHECK_THINGS_IN_TEMP_DIR_EXCLUDE_="^ompi"
+ENV _R_CHECK_BASHISMS_ true
+ENV _R_CHECK_DEPENDS_ONLY_DATA_ true
+ENV _R_CHECK_MATRIX_DATA_ TRUE
+ENV _R_CHECK_RD_VALIDATE_RD2HTML_ true
+ENV _R_CHECK_RD_MATH_RENDERING_ true
+
+# ------------------------------------------------------------------------------------
+# Check config, no need to check the PDF manual and vignettes here.
+# We also avoid that bashism checks, as it needs external tools.
+
+ENV _R_CHECK_TESTS_NLINES_="0"
+ENV CHECK_ARGS="--no-manual --no-build-vignettes"
+ENV _R_CHECK_BASHISMS_=false
+
+# Support R CMD INSTALL --use-LTO ., similarly to CRAN at https://www.stats.ox.ac.uk/pub/bdr/LTO/README.txt
+RUN echo -e '# Support --use-LTO\nLTO_OPT = -flto=10\nLTO_FC_OPT = -flto=10' >> /opt/R/devel-gcc15/lib/R/etc/Makeconf
diff --git a/containers/gcc15/r-check b/containers/gcc15/r-check
@@ -0,0 +1,18 @@
+#! /bin/bash
+set -e
+
+checkdir=${1-/check}
+
+do_check () {
+    pkg=${1}
+    echo Checking "$pkg"
+    (
+        cd `dirname $pkg`
+        R -q -e "pak::pkg_install('deps::$pkg', dependencies = TRUE)"
+        R CMD check $CHECK_ARGS	$pkg
+    )
+}
+
+for pkg in `ls $checkdir/*.tar.gz`; do
+    do_check "$pkg"
+done
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -120,6 +120,20 @@ services:
     volumes:
       - ./integration/tmp:/tmp/output
 
+  fedora-gcc15:
+    platform: linux/amd64
+    command: ./build.sh
+    environment:
+      - R_VERSION=devel
+      - R_TYPE=-gcc15
+      - LOCAL_STORE=/tmp/output
+    build:
+      context: .
+      dockerfile: builder/Dockerfile.fedora-gcc15
+    image: rhub/fedora-gcc15:latest
+    volumes:
+      - ./integration/tmp:/tmp/output
+
   fedora-mkl:
     platform: linux/amd64
     command: ./build.sh