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ARROW-14910: [R] [CI] Use dev duckdb to build with < 8GB or ram #11795

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jonkeane wants to merge 8 commits into from
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ARROW-14910: [R] [CI] Use dev duckdb to build with < 8GB or ram #11795

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d154939
move duckdb to remotes
jonkeane Nov 29, 2021
0635fa8
A different tactic
jonkeane Nov 29, 2021
c25d769
oops
jonkeane Nov 29, 2021
b108c8c
set the python symlinks before R deps
jonkeane Nov 29, 2021
0b77162
also need to link python in linuc-r.dockerfile
jonkeane Nov 29, 2021
a660b47
Use RSPM binary if it's in the repos
jonkeane Nov 30, 2021
5be557c
Update ci/scripts/r_deps.sh
jonkeane Nov 30, 2021
a1d4a07
Skip flaky DuckDB roundtrip for now
jonkeane Nov 30, 2021
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8 changes: 4 additions & 4 deletions ci/docker/linux-apt-r.dockerfile
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Expand Up @@ -84,6 +84,10 @@ RUN cat /arrow/ci/etc/rprofile >> $(R RHOME)/etc/Rprofile.site
# Also ensure parallel compilation of C/C++ code
RUN echo "MAKEFLAGS=-j$(R -s -e 'cat(parallel::detectCores())')" >> $(R RHOME)/etc/Renviron.site

# Set up Python 3 and its dependencies
RUN ln -s /usr/bin/python3 /usr/local/bin/python && \
ln -s /usr/bin/pip3 /usr/local/bin/pip

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@jonkeane jonkeane Nov 30, 2021

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Installing duckdb from source (at least from github) requires the use of Python, so we need to make sure that we have a python on the path before we do that step (for now).

COPY ci/scripts/r_deps.sh /arrow/ci/scripts/
COPY r/DESCRIPTION /arrow/r/
RUN /arrow/ci/scripts/r_deps.sh /arrow
Expand All @@ -93,10 +97,6 @@ RUN /arrow/ci/scripts/install_minio.sh ${arch} linux latest /usr/local
COPY ci/scripts/install_gcs_testbench.sh /arrow/ci/scripts/
RUN /arrow/ci/scripts/install_gcs_testbench.sh ${arch} default

# Set up Python 3 and its dependencies
RUN ln -s /usr/bin/python3 /usr/local/bin/python && \
ln -s /usr/bin/pip3 /usr/local/bin/pip

COPY python/requirements-build.txt /arrow/python/
RUN pip install -r arrow/python/requirements-build.txt

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4 changes: 4 additions & 0 deletions ci/docker/linux-r.dockerfile
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Expand Up @@ -46,6 +46,10 @@ COPY ci/scripts/install_minio.sh /arrow/ci/scripts/
COPY ci/scripts/install_gcs_testbench.sh /arrow/ci/scripts/
RUN /arrow/ci/scripts/r_docker_configure.sh

# Set up Python 3 and its dependencies
RUN ln -s /usr/bin/python3 /usr/local/bin/python && \
ln -s /usr/bin/pip3 /usr/local/bin/pip

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@jonkeane jonkeane Nov 30, 2021

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Same above, Python(3) was already installed, but it isn't on the path as python so the duckdb source install bails

COPY ci/scripts/r_deps.sh /arrow/ci/scripts/
COPY r/DESCRIPTION /arrow/r/
RUN /arrow/ci/scripts/r_deps.sh /arrow
9 changes: 9 additions & 0 deletions ci/scripts/r_deps.sh
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Expand Up @@ -41,6 +41,15 @@ fi
# but we want to error/fail the build.
# options(warn=2) turns warnings into errors
${R_BIN} -e "options(warn=2); install.packages('remotes'); remotes::install_cran(c('glue', 'rcmdcheck', 'sys')); remotes::install_deps(INSTALL_opts = '"${INSTALL_ARGS}"')"

# (Temporarily) install DuckDB from source to avoid their Unity builds
# (though only if we haven't filtered it out of the deps above,
# and if we can't get a binary from RSPM)
# Remove when there is a DuckDB release > 0.3.1-1
if grep -q "duckdb" DESCRIPTION; then
${R_BIN} -e "if (all(!grepl('packagemanager.rstudio', options('repos')))) { remotes::install_github('duckdb/duckdb', subdir = '/tools/rpkg', build = FALSE) }"
fi

# Separately install the optional/test dependencies but don't error on them,
# they're not available everywhere and that's ok
${R_BIN} -e "remotes::install_deps(dependencies = TRUE, INSTALL_opts = '"${INSTALL_ARGS}"')"
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1 change: 1 addition & 0 deletions r/tests/testthat/test-duckdb.R
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Expand Up @@ -66,6 +66,7 @@ test_that("to_duckdb", {
})

test_that("to_duckdb then to_arrow", {
skip("Flaky, unskip when ARROW-14745 is merged")
ds <- InMemoryDataset$create(example_data)

ds_rt <- ds %>%
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