diff --git a/docker/Dockerfile-alpine-320 b/docker/Dockerfile-alpine-320 index 974edcf..76b7341 100644 --- a/docker/Dockerfile-alpine-320 +++ b/docker/Dockerfile-alpine-320 @@ -28,13 +28,15 @@ RUN apk del lapack lapack-dev # libxml2-dev: xml2 # libgit2-dev: gert # libpq-dev: RPostgres -RUN apk add -q --no-cache R-dev curl ca-certificates bash g++ tzdata openjdk17 tar sed patch openblas-dev pkgconfig linux-headers ccache libxml2-dev libgit2-dev libpq-dev pkgconfig +# libfftw3-dev: ravetools -> actually auto-detect but somehow doesn't work in container? +RUN apk add -q --no-cache R-dev curl ca-certificates bash g++ tzdata openjdk17 tar sed patch openblas-dev pkgconfig linux-headers ccache libxml2-dev libgit2-dev libpq-dev pkgconfig fftw-dev # https://github.com/RcppCore/Rcpp/issues/448#issuecomment-220148774 # LDFLAGS+=-fPIC -> arrow (https://github.com/r-hub/r-minimal/blob/main/examples/arrow/Dockerfile) # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66) # CXXFLAGS: -> Rcpp -RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCXXFLAGS=-D__MUSL__\nCPPFLAGS=-D__MUSL__\nCFLAGS += -flax-vector-conversions\nLDFLAGS+=-fPIC\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=ccache /usr/bin/gfortran\nFC=ccache /usr/bin/gfortran" > /root/.R/Makevars' +# can't set ccache for gfortran because of https://gitlab.com/roigrp/solver/highs/-/issues/4 +RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCXXFLAGS=-D__MUSL__\nCPPFLAGS=-D__MUSL__\nCFLAGS += -flax-vector-conversions\nLDFLAGS+=-fPIC\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=gfortran\nFC=gfortran" > /root/.R/Makevars' # R repos RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > /root/.Rprofile' diff --git a/docker/Dockerfile-redhat-8 b/docker/Dockerfile-redhat-8 index 3c32bd5..a7fb084 100644 --- a/docker/Dockerfile-redhat-8 +++ b/docker/Dockerfile-redhat-8 @@ -18,7 +18,9 @@ RUN subscription-manager register --username mail@devxy.io --password "$RED_HAT_ RUN dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm && dnf install -y epel-release # xvfb: for graphical pkgs requiring tcl, like gWidgets2tcltk # ImageMagick-c++-devel ImageMagick-devel: boths are not auto-installed via pak sysreqs -RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb ImageMagick-c++-devel ImageMagick-devel xz pkg-config +# mecab-devel: RcppMeCab -> no autodetection yet +# libfftw3-dev: ravetools -> actually auto-detect but somehow doesn't work in container? +RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb ImageMagick-c++-devel ImageMagick-devel xz pkg-config mecab-devel fftw-devel ### CUSTOM DEPENDENCIES # These usually are not packaged in OS repositories and need to be installed from source @@ -32,7 +34,8 @@ RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/ ### Makevars # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66) -RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCFLAGS += -flax-vector-conversions\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=ccache /usr/bin/gfortran\nFC=ccache /usr/bin/gfortran" >> /root/.R/Makevars' +# can't set ccache for gfortran because of https://gitlab.com/roigrp/solver/highs/-/issues/4 +RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCFLAGS += -flax-vector-conversions\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=gfortran\nFC=gfortran" >> /root/.R/Makevars' # R repos RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > /root/.Rprofile' diff --git a/docker/Dockerfile-redhat-9 b/docker/Dockerfile-redhat-9 index ce7f328..bd67051 100644 --- a/docker/Dockerfile-redhat-9 +++ b/docker/Dockerfile-redhat-9 @@ -18,7 +18,9 @@ RUN subscription-manager register --username mail@devxy.io --password "$RED_HAT_ RUN dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm && dnf install -y epel-release # xvfb: for graphical pkgs requiring tcl, like gWidgets2tcltk # ImageMagick-c++-devel ImageMagick-devel: boths are not auto-installed via pak sysreqs -RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb tk-devel ImageMagick-c++-devel ImageMagick-devel xz pkg-config +# mecab-devel: RcppMeCab -> no autodetection yet +# libfftw3-dev: ravetools -> actually auto-detect but somehow doesn't work in container? +RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb tk-devel ImageMagick-c++-devel ImageMagick-devel xz pkg-config mecab-devel fftw-devel ### CUSTOM DEPENDENCIES # These usually are not packaged in OS repositories and need to be installed from source @@ -32,7 +34,8 @@ RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/ ### Makevars # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66) -RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCFLAGS += -flax-vector-conversions\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=ccache /usr/bin/gfortran\nFC=ccache /usr/bin/gfortran" >> /root/.R/Makevars' +# can't set ccache for gfortran because of https://gitlab.com/roigrp/solver/highs/-/issues/4 +RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCFLAGS += -flax-vector-conversions\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=gfortran\nFC=gfortran" >> /root/.R/Makevars' # R repos RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > /root/.Rprofile' diff --git a/docker/Dockerfile-ubuntu-2204 b/docker/Dockerfile-ubuntu-2204 index 70b75ac..3e077ef 100644 --- a/docker/Dockerfile-ubuntu-2204 +++ b/docker/Dockerfile-ubuntu-2204 @@ -16,7 +16,9 @@ ARG GITHUB_PAT # xvfb: for graphical pkgs requiring tcl, like gWidgets2tcltk # tcl tk tk-dev tk-table: must be available before running xvfb-run (i.e. starting the graphical session) -RUN apt update && apt install -y --no-install-recommends gdebi-core g++ gfortran libbz2-dev libblas-dev libicu-dev liblapack-dev liblzma-dev libpaper-utils libpcre2-dev libtcl8.6 libtk8.6 libxt6 unzip zip zlib1g-dev libpcre3-dev libopenblas-dev curl ca-certificates make ccache htop libgit2-dev git libpq-dev libxml2-dev libgit2-dev cmake xvfb libcurl4-openssl-dev xz-utils tcl tk tk-dev tk-table pkg-config +# libmecab-dev: RcppMeCab -> no autodetection yet +# libfftw3-dev: ravetools -> actually auto-detect but somehow doesn't work in container? +RUN apt update && apt install -y --no-install-recommends gdebi-core g++ gfortran libbz2-dev libblas-dev libicu-dev liblapack-dev liblzma-dev libpaper-utils libpcre2-dev libtcl8.6 libtk8.6 libxt6 unzip zip zlib1g-dev libpcre3-dev libopenblas-dev curl ca-certificates make ccache htop libgit2-dev git libpq-dev libxml2-dev libgit2-dev cmake xvfb libcurl4-openssl-dev xz-utils tcl tk tk-dev tk-table pkg-config libmecab-dev libfftw3-dev ### CUSTOM DEPENDENCIES # These usually are not packaged in OS repositories and need to be installed from source @@ -30,7 +32,8 @@ RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/ ### Makevars # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66) -RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCFLAGS += -flax-vector-conversions\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=ccache /usr/bin/gfortran\nFC=ccache /usr/bin/gfortran" >> /root/.R/Makevars' +# can't set ccache for gfortran because of https://gitlab.com/roigrp/solver/highs/-/issues/4 +RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCFLAGS += -flax-vector-conversions\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=gfortran\nFC=gfortran" >> /root/.R/Makevars' # R repos RUN bash -c 'echo -e "options(pkg.sysreqs_verbose = TRUE, crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > ~/.Rprofile' diff --git a/docker/Dockerfile-ubuntu-2404 b/docker/Dockerfile-ubuntu-2404 index ee62f7b..9bd47b5 100644 --- a/docker/Dockerfile-ubuntu-2404 +++ b/docker/Dockerfile-ubuntu-2404 @@ -16,7 +16,9 @@ ARG GITHUB_PAT # xvfb: for graphical pkgs requiring tcl, like gWidgets2tcltk # tcl tk tk-dev tk-table: must be available before running xvfb-run (i.e. starting the graphical session) -RUN apt update && apt install -y --no-install-recommends gdebi-core g++ gfortran libbz2-dev libblas-dev libicu-dev liblapack-dev liblzma-dev libpaper-utils libpcre2-dev libtcl8.6 libtk8.6 libxt6 unzip zip zlib1g-dev libpcre3-dev libopenblas-dev curl ca-certificates make ccache htop libgit2-dev git libpq-dev libxml2-dev libgit2-dev cmake xvfb libcurl4-openssl-dev xz-utils tcl tk tk-dev tk-table pkg-config +# libmecab-dev: RcppMeCab -> no autodetection yet +# libfftw3-dev: ravetools -> actually auto-detect but somehow doesn't work in container? +RUN apt update && apt install -y --no-install-recommends gdebi-core g++ gfortran libbz2-dev libblas-dev libicu-dev liblapack-dev liblzma-dev libpaper-utils libpcre2-dev libtcl8.6 libtk8.6 libxt6 unzip zip zlib1g-dev libpcre3-dev libopenblas-dev curl ca-certificates make ccache htop libgit2-dev git libpq-dev libxml2-dev libgit2-dev cmake xvfb libcurl4-openssl-dev xz-utils tcl tk tk-dev tk-table pkg-config libmecab-dev libfftw3-dev ### CUSTOM DEPENDENCIES # These usually are not packaged in OS repositories and need to be installed from source @@ -30,7 +32,8 @@ RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/ ### Makevars # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66) -RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCFLAGS += -flax-vector-conversions\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=ccache /usr/bin/gfortran\nFC=ccache /usr/bin/gfortran" >> /root/.R/Makevars' +# can't set ccache for gfortran because of https://gitlab.com/roigrp/solver/highs/-/issues/4 +RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCFLAGS += -flax-vector-conversions\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=gfortran\nFC=gfortran" >> /root/.R/Makevars' # R repos RUN bash -c 'echo -e "options(pkg.sysreqs_verbose = TRUE, crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > ~/.Rprofile'