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# Workflow is triggered on label and check installation on various operating systems | ||
# This action is adapted from https://github.com/t4d-gmbh/stubbed_versioning | ||
name: Fedora Install | ||
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on: | ||
push: | ||
branches: | ||
- "main" | ||
- "117-elaborate-if-inla-jags-and-gsl-can-be-installed-via-systemrequirements" | ||
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env: | ||
JAGS: '4.3.2' | ||
BUILD_LOC: "./build" | ||
BRANCH: ${{ github.head_ref || github.ref_name }} | ||
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permissions: | ||
packages: read | ||
contents: write | ||
pull-requests: write | ||
repository-projects: write | ||
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jobs: | ||
setup-and-install: | ||
runs-on: ubuntu-latest | ||
container: | ||
image: "fedora:latest" | ||
name: fedora-latest R release | ||
env: | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
R_KEEP_PKG_SOURCE: yes | ||
steps: | ||
- name: prepare fedora | ||
run: | | ||
dnf -y install wget | ||
dnf -y install gcc | ||
dnf -y install gcc-c++ | ||
dnf -y install gfortran | ||
dnf -y install lapack* # is needed on fedora server | ||
dnf -y install blas* | ||
dnf -y install atlas* | ||
- name: install R | ||
run: | | ||
dnf -y install R | ||
- name: install config and build dependencies | ||
run: | | ||
dnf -y install pkg-config | ||
dnf -y install cmake | ||
dnf -y install R-devtools | ||
- name: install GSL | ||
run: | | ||
dnf -y install gsl-devel | ||
- name: install JAGS | ||
run: | | ||
wget -O /tmp/jags.tar.gz https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-${{ env.JAGS }}.tar.gz/download | ||
cd /tmp | ||
tar -xf jags.tar.gz | ||
cd /tmp/JAGS-${{ env.JAGS }} | ||
./configure --libdir=/usr/local/lib64 | ||
make | ||
make install | ||
- name: assert runtime linkage | ||
run: | | ||
echo "/usr/local/lib64" > /etc/ld.so.conf.d/jags.conf | ||
/sbin/ldconfig | ||
- name: install rjags | ||
run: | | ||
install.packages("rjags", configure.args="--enable-rpath", repos=c(CRAN="https://cran.r-project.org")) | ||
library("rjags") | ||
shell: Rscript {0} | ||
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- name: installing dependencies from BiocManager | ||
run: | | ||
if (!requireNamespace("BiocManager", quietly = TRUE)) | ||
install.packages("BiocManager", repos=c(CRAN="https://cran.r-project.org")) | ||
BiocManager::install("Rgraphviz") | ||
BiocManager::install("graph") | ||
shell: Rscript {0} | ||
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- name: pak install from GitHub | ||
run: | | ||
install.packages('pak', repos=c(CRAN="https://cran.r-project.org")) | ||
pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}") | ||
library('abn') | ||
shell: Rscript {0} | ||
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- name: fetch the repository from GitHub | ||
uses: actions/checkout@v4 | ||
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- name: deactivate the renv | ||
run: | | ||
renv::deactivate() | ||
shell: Rscript {0} | ||
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- name: install from source | ||
run: | | ||
pak::local_install(dependencies=TRUE) | ||
shell: Rscript {0} | ||
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- name: run the tests | ||
run: | | ||
pak::pak('r-lib/testthat') | ||
testthat::test_local(path='tests', load_package='none') | ||
shell: Rscript {0} | ||
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