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Updated parts of the bundled HDF5 configure scripts (config.guess & config.sub) which were very old and didn't recognise Apple arm64 systems when running R installed via conda. (Thanks to @eyalbenda for reporting. Fixes #54.
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,41 @@ | ||
on: | ||
push: | ||
workflow_dispatch: | ||
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name: OSX and Conda | ||
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env: | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
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jobs: | ||
test-pkg: | ||
runs-on: macOS-14 | ||
name: testing conda | ||
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steps: | ||
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- uses: actions/checkout@v4 | ||
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- uses: conda-incubator/setup-miniconda@v3 | ||
with: | ||
use-mamba: true | ||
miniconda-version: "latest" | ||
channels: conda-forge,defaults,bioconda | ||
channel-priority: true | ||
activate-environment: foo | ||
architecture: arm64 | ||
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- name: Bash | ||
shell: bash -el {0} | ||
run: | | ||
conda install -c r r-biocmanager r-remotes | ||
- name: Install Rhdf5lib from source | ||
shell: bash -el {0} | ||
run: | | ||
mkdir ${{ runner.temp }}/R-lib | ||
R CMD INSTALL --library=${{ runner.temp }}/R-lib ${{ github.workspace }} | ||
working-directory: ${{ runner.temp }} | ||
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@@ -1,8 +1,10 @@ | ||
on: | ||
push: | ||
branches-ignore: | ||
- mac-conda | ||
pull_request: | ||
branches: | ||
- master | ||
- devel | ||
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name: R-CMD-check | ||
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@@ -19,10 +21,11 @@ jobs: | |
fail-fast: false | ||
matrix: | ||
config: | ||
- { os: windows-2022, bioc-version: 'devel'} | ||
- { os: macOS-latest, bioc-version: 'devel'} | ||
- { os: ubuntu-20.04, bioc-version: 'devel', system-libs: 'libcurl4-gnutls-dev libaec-dev'} | ||
- { os: ubuntu-22.04, bioc-version: 'devel', system-libs: 'libcurl4-openssl-dev'} | ||
- { os: windows-2022, bioc-version: 'devel', Ncpus: 4} | ||
- { os: macOS-13, bioc-version: 'devel', Ncpus: 4} | ||
- { os: macOS-14, bioc-version: 'devel', Ncpus: 3} | ||
- { os: ubuntu-20.04, bioc-version: 'devel', Ncpus: 4, system-libs: 'libcurl4-gnutls-dev libaec-dev'} | ||
- { os: ubuntu-22.04, bioc-version: 'devel', Ncpus: 4, system-libs: 'libcurl4-openssl-dev'} | ||
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steps: | ||
- name: Configure git | ||
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@@ -41,21 +44,15 @@ jobs: | |
install.libs("openssl") | ||
shell: Rscript {0} | ||
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- uses: actions/checkout@v3 | ||
- uses: actions/checkout@v4 | ||
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- name: Setup R and Bioconductor | ||
uses: grimbough/bioc-actions/setup-bioc@v1 | ||
with: | ||
bioc-version: ${{ matrix.config.bioc-version }} | ||
bioc-mirror: https://ftp.gwdg.de/pub/misc/bioconductor | ||
Ncpus: ${{ matrix.config.Ncpus }} | ||
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# - name: Create Makevars | ||
# if: ${{ matrix.config.os == 'macOS-latest' }} | ||
# run: | | ||
# mkdir $HOME/.R | ||
# echo 'LDFLAGS="-L/usr/local/opt/[email protected]/lib"' > $HOME/.R/Makevars | ||
# echo 'CPPFLAGS="-I/usr/local/opt/[email protected]/include"' >> $HOME/.R/Makevars | ||
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- uses: r-lib/actions/setup-pandoc@v2 | ||
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- name: Install dependencies | ||
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@@ -82,14 +79,14 @@ jobs: | |
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- name: Upload check results | ||
if: always() | ||
uses: actions/upload-artifact@v3 | ||
uses: actions/upload-artifact@v4 | ||
with: | ||
name: ${{ matrix.config.os }}-results | ||
path: ${{ steps.build-install-check.outputs.check-dir }} | ||
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- name: Upload check results | ||
if: ${{ failure() }} | ||
uses: actions/upload-artifact@v3 | ||
uses: actions/upload-artifact@v4 | ||
with: | ||
name: ${{ matrix.config.os }}-${{ matrix.config.r }}-hdf5_config.log | ||
path: check/*.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/config.log |
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