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[r] Use lower and upper pin bounds on tiledb-r for release-1.9 branch #2374

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merged 10 commits into from
Apr 17, 2024
Merged

[r] Use lower and upper pin bounds on tiledb-r for release-1.9 branch #2374

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33286fd
[r] Experiment with bidirectional-pin syntax
johnkerl Apr 3, 2024
1394740
[r] Experiment with bidirectional-pin syntax
johnkerl Apr 3, 2024
3c1188d
Update apis/r/DESCRIPTION
johnkerl Apr 16, 2024
4d75027
experimental commit to look for green CI with new technique
johnkerl Apr 16, 2024
c8e402d
neaten
johnkerl Apr 16, 2024
2b375e7
Add missing comma
eddelbuettel Apr 16, 2024
37e1b7e
[r/ci] Required changes to `r-ci.yml`, plus simplifications (#2450)
eddelbuettel Apr 17, 2024
049af1c
restore useful debugs after merge
johnkerl Apr 17, 2024
fe8d232
code-review feedback
johnkerl Apr 17, 2024
3cb2e01
code-review feedback
johnkerl Apr 17, 2024
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56 changes: 27 additions & 29 deletions .github/workflows/r-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -61,37 +61,26 @@ jobs:
run: cd apis/r && tools/r-ci.sh install_bioc SingleCellExperiment


- name: Install 0.25 build of tiledb-r with core 2.21
run: |
cd apis/r
wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz
Rscript -e 'remotes::install_deps("0.25.0.tar.gz")'
R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by TileDB-SOMA 1.9

# Uncomment these next two stanzas as needed whenever we've just released a new tiledb-r for
# which source is available but CRAN releases (and hence update r2u binaries) are not yet:
#
# IMPORTANT: these two stanzas should remain uncommented _only_ during the propagation time
# between (a) publication of source for a new TileDB-R _upon which_ TileDB-SOMA depends in its
# apis/R/DESCRIPTION file and (b) appearance of binaries.
#
# Please see https://github.com/single-cell-data/TileDB-SOMA/wiki/Branches-and-releases which
# is crucial for anyone doing releases of TileDB-SOMA.
#
# Please edit both files in the same way:
# * r-ci.yml
# * r-python-interop-testing.yml
# As documented there, we have a cadence for updating tiledb-inc.r-universe.dev.
#
# Please also see https://github.com/single-cell-data/TileDB-SOMA/issues/2447 regarding R CI YAML.
#
# Please also see https://github.com/single-cell-data/TileDB-SOMA/issues/2406 regarding
# our upcoming elimination of TileDB-SOMA's dependency on TileDB-R entirely.
#
# Do not remove these comments until such time as we have eliminated our dependency on
# the TileDB-R package.

#- 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'))"
- 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://tiledb-inc.r-universe.dev', 'https://cloud.r-project.org'))"

#- 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: 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://tiledb-inc.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
Expand All @@ -116,12 +105,21 @@ jobs:
- name: Update Packages
run: Rscript -e 'update.packages(ask=FALSE)'

- name: Re-install 0.25 build of tiledb-r with core 2.21
run: |
cd apis/r
wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz
Rscript -e 'remotes::install_deps("0.25.0.tar.gz")'
R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by SOMA 1.9
# WIP (NOT READY FOR REVIEW) -- LOOKING FOR GREEN CI
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#- name: Install 0.25 build of tiledb-r with core 2.21
# run: |
# cd apis/r
# wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz
# Rscript -e 'remotes::install_deps("0.25.0.tar.gz")'
# R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by TileDB-SOMA 1.9

# WIP (NOT READY FOR REVIEW) -- LOOKING FOR GREEN CI
#- name: Re-install 0.25 build of tiledb-r with core 2.21
# run: |
# cd apis/r
# wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz
# Rscript -e 'remotes::install_deps("0.25.0.tar.gz")'
# R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by SOMA 1.9

# - name: Build Package
# run: cd apis/r && R CMD build --no-build-vignettes --no-manual .
Expand Down
54 changes: 26 additions & 28 deletions .github/workflows/r-python-interop-testing.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,37 +41,34 @@ jobs:
- name: MkVars
run: mkdir ~/.R && echo "CXX17FLAGS=-Wno-deprecated-declarations -Wno-deprecated" > ~/.R/Makevars

- name: Install 0.25 build of tiledb-r with core 2.21
run: |
cd apis/r
wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz
Rscript -e 'remotes::install_deps("0.25.0.tar.gz")'
R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by TileDB-SOMA 1.9
# WIP (NOT READY FOR REVIEW) -- LOOKING FOR GREEN CI
#- name: Install 0.25 build of tiledb-r with core 2.21
# run: |
# cd apis/r
# wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz
# Rscript -e 'remotes::install_deps("0.25.0.tar.gz")'
# R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by TileDB-SOMA 1.9

# Uncomment these next two stanzas as needed whenever we've just released a new tiledb-r for
# which source is available but CRAN releases (and hence update r2u binaries) are not yet:
#
# IMPORTANT: these two stanzas should remain uncommented _only_ during the propagation time
# between (a) publication of source for a new TileDB-R _upon which_ TileDB-SOMA depends in its
# apis/R/DESCRIPTION file and (b) appearance of binaries.
#
# Please see https://github.com/single-cell-data/TileDB-SOMA/wiki/Branches-and-releases which
# is crucial for anyone doing releases of TileDB-SOMA.
#
# Please edit both files in the same way:
# * r-ci.yml
# * r-python-interop-testing.yml
# As documented there, we have a cadence for updating tiledb-inc.r-universe.dev.
#
# Please also see https://github.com/single-cell-data/TileDB-SOMA/issues/2447 regarding R CI YAML.
#
# Please also see https://github.com/single-cell-data/TileDB-SOMA/issues/2406 regarding
# our upcoming elimination of TileDB-SOMA's dependency on TileDB-R entirely.
#
# Do not remove these comments until such time as we have eliminated our dependency on
# the TileDB-R package.

#- 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'))"
- 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://tiledb-inc.r-universe.dev', 'https://cloud.r-project.org'))"

#- 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: 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://tiledb-inc.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))"

- name: Build and install libtiledbsoma
run: sudo scripts/bld --prefix=/usr/local && sudo ldconfig
Expand Down Expand Up @@ -107,12 +104,13 @@ jobs:
- name: Update Packages
run: Rscript -e 'update.packages(ask=FALSE)'
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- name: Re-install 0.25 build of tiledb-r with core 2.21
run: |
cd apis/r
wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz
Rscript -e 'remotes::install_deps("0.25.0.tar.gz")'
R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by SOMA 1.9
# WIP (NOT READY FOR REVIEW) -- LOOKING FOR GREEN CI
#- name: Re-install 0.25 build of tiledb-r with core 2.21
# run: |
# cd apis/r
# wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz
# Rscript -e 'remotes::install_deps("0.25.0.tar.gz")'
# R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by SOMA 1.9
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- name: Show package versions
run: |
Expand Down
2 changes: 1 addition & 1 deletion apis/r/DESCRIPTION
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Expand Up @@ -34,7 +34,7 @@ Imports:
Matrix,
stats,
bit64,
tiledb (>= 0.25.0),
tiledb (>= 0.25.0), tiledb (<= 0.25.0.5)
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arrow,
utils,
fs,
Expand Down
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