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[ci/r] Use TileDB-R 0.21.1 binaries (#1738)
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* [ci/r] Use TileDB-R 0.21.1 binaries

* CI from 1749

* code-review feedback
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johnkerl authored and github-actions[bot] committed Oct 2, 2023
1 parent 8ff82bd commit 6aba78d
Showing 1 changed file with 19 additions and 9 deletions.
28 changes: 19 additions & 9 deletions .github/workflows/r-ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -41,15 +41,25 @@ jobs:
- name: Install BioConductor package SingleCellExperiment
run: cd apis/r && tools/r-ci.sh install_bioc SingleCellExperiment

# Given propagation delay for binaries at https://r2u.stat.illinois.edu/ubuntu/pool/dists/jammy/main/
- name: Install r-universe build of tiledb-r (macOS)
if: ${{ matrix.os == 'macOS-latest' }}
run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev', 'https://cloud.r-project.org'))"

# Given propagation delay for binaries at https://r2u.stat.illinois.edu/ubuntu/pool/dists/jammy/main/
- name: Install r-universe build of tiledb-r (linux)
if: ${{ matrix.os != 'macOS-latest' }}
run: cd apis/r && Rscript -e "options(bspm.version.check=TRUE); install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))"
# The next two stanzas are necessary given propagation delay for binaries at
# https://r2u.stat.illinois.edu/ which may lack binaries (for short periods of usually a day)
# when sources have been updated. The default installation could switch to installation from
# sources --- but that would require installing all build dependencies. To see what the most
# recent binary is run e.g. docker run --rm -ti rocker/r2u bash -c 'apt update -qq &&
# apt-cache show r-cran-tiledb' Using the r-universe builds (as below) is a suitable fallback
# as they update more frequently than CRAN.

# Uncomment these next two stanzas as needed whenever we've just released a new tiledb-r for
# which source is available but binaries are not yet:

#- name: Install r-universe build of tiledb-r (macOS)
# if: ${{ matrix.os == 'macOS-latest' }}
# run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev', 'https://cloud.r-project.org'))"

# docker run --rm -ti rocker/r2u Rscript -e 'install.packages("tiledb")'
#- name: Install r-universe build of tiledb-r (linux)
# if: ${{ matrix.os != 'macOS-latest' }}
# run: cd apis/r && Rscript -e "options(bspm.version.check=TRUE); install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))"

- name: Dependencies
run: cd apis/r && tools/r-ci.sh install_all
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