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Posted to github@arrow.apache.org by "thisisnic (via GitHub)" <gi...@apache.org> on 2025/10/31 10:55:57 UTC
[PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
thisisnic opened a new pull request, #48014:
URL: https://github.com/apache/arrow/pull/48014
### Rationale for this change
In the R package we use bundled RE2 to build from source, but it doesn't work on Alpine Linux - we should allow system RE2 when building there.
### What changes are included in this PR?
Add CI job and update nixlibs to allow building using system RE2
### Are these changes tested?
They'll be tested on CI
### Are there any user-facing changes?
No
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3596865208
@github-actions crossbow submit test-r-alpine-linux-cran
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3665807994
@github-actions crossbow submit test-r-alpine-linux-cran
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3481535614
@github-actions crossbow submit test-r-alpine-linux
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3481625341
Revision: 97dd549ef6b0d78f4f0e12f5c99dd18033939ef0
Submitted crossbow builds: [ursacomputing/crossbow @ actions-5ba8e7e3d4](https://github.com/ursacomputing/crossbow/branches/all?query=actions-5ba8e7e3d4)
|Task|Status|
|----|------|
|test-r-alpine-linux|[](https://github.com/ursacomputing/crossbow/actions/runs/19043041213/job/54384574607)|
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on code in PR #48014:
URL: https://github.com/apache/arrow/pull/48014#discussion_r2627675390
##########
ci/scripts/r_test.sh:
##########
@@ -101,7 +101,7 @@ SCRIPT="as_cran <- !identical(tolower(Sys.getenv('NOT_CRAN')), 'true')
build_args <- '--no-build-vignettes'
}
- if (!as_cran && requireNamespace('reticulate', quietly = TRUE) && reticulate::py_module_available('pyarrow')) {
+ if (!as_cran && (requireNamespace('reticulate', quietly = TRUE)) && reticulate::py_module_available('pyarrow')) {
Review Comment:
Hmm...they don't - I tried it locally before/after, and whatever was invoking a Python module install must have succeeded when I ran the "before" version, and so when I ran it again "after", I conflated the change in the environment (and thus no console output) with the code change working.
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3665058286
Revision: b4f611c488551d6f56fd993ec455bbc3381f0ee3
Submitted crossbow builds: [ursacomputing/crossbow @ actions-65f1d7dddc](https://github.com/ursacomputing/crossbow/branches/all?query=actions-65f1d7dddc)
|Task|Status|
|----|------|
|test-r-alpine-linux-cran|[](https://github.com/ursacomputing/crossbow/actions/runs/20302287891/job/58310623498)|
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3665050074
@github-actions crossbow submit test-r-alpine-linux-cran
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3591511373
@github-actions crossbow submit test-r-alpine-linux
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on code in PR #48014:
URL: https://github.com/apache/arrow/pull/48014#discussion_r2611802798
##########
ci/docker/alpine-linux-3.22-r.dockerfile:
##########
@@ -0,0 +1,88 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+# Minimal Alpine Linux container with R for testing Arrow R package
+# on musl libc (CRAN runs checks on Alpine Linux 3.22)
+# Replicates CRAN's Alpine environment as closely as possible
+
+ARG arch=amd64
+FROM ${arch}/alpine:3.22
+
+# Install R and essential build tools
+# Note: bash is needed for Arrow CI scripts, even though CRAN's Alpine uses BusyBox
+RUN apk add \
+ R \
+ R-dev \
+ R-doc \
+ bash \
+ checkbashisms \
+ cmake \
+ curl-dev \
+ g++ \
+ gcc \
+ git \
+ linux-headers \
+ make \
+ musl-locales \
+ openssl-dev \
Review Comment:
`curl-dev` and `openssl-dev` are both here and in `ci/scripts/r_install_system_dependences.sh` - should it only be in 1?
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on code in PR #48014:
URL: https://github.com/apache/arrow/pull/48014#discussion_r2611802798
##########
ci/docker/alpine-linux-3.22-r.dockerfile:
##########
@@ -0,0 +1,88 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+# Minimal Alpine Linux container with R for testing Arrow R package
+# on musl libc (CRAN runs checks on Alpine Linux 3.22)
+# Replicates CRAN's Alpine environment as closely as possible
+
+ARG arch=amd64
+FROM ${arch}/alpine:3.22
+
+# Install R and essential build tools
+# Note: bash is needed for Arrow CI scripts, even though CRAN's Alpine uses BusyBox
+RUN apk add \
+ R \
+ R-dev \
+ R-doc \
+ bash \
+ checkbashisms \
+ cmake \
+ curl-dev \
+ g++ \
+ gcc \
+ git \
+ linux-headers \
+ make \
+ musl-locales \
+ openssl-dev \
Review Comment:
`curl-dev` and `openssl-dev` are both here and in `ci/scripts/r_install_system_dependences.sh` - should it only be in 1?
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3596204547
@github-actions crossbow submit test-r-alpine-linux-cran
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3591559732
Revision: ecbbdca705fa9d3f76bc99257db757c9315319ef
Submitted crossbow builds: [ursacomputing/crossbow @ actions-08f242cfb4](https://github.com/ursacomputing/crossbow/branches/all?query=actions-08f242cfb4)
|Task|Status|
|----|------|
|test-r-alpine-linux|[](https://github.com/ursacomputing/crossbow/actions/runs/19782889814/job/56685455667)|
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3591601982
Revision: 8f2a047b6f46fc356f78d7cb7443cfa46187102d
Submitted crossbow builds: [ursacomputing/crossbow @ actions-41ea6bbf02](https://github.com/ursacomputing/crossbow/branches/all?query=actions-41ea6bbf02)
|Task|Status|
|----|------|
|test-r-alpine-linux|[](https://github.com/ursacomputing/crossbow/actions/runs/19783436590/job/56686672198)|
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3645560285
My bad @nealrichardson, the approach here morphed a bit over time since the original issue that I opened.
Now we have bumped our bundled version of RE2 to be compatible with Alpine in #48011, I don't think we need to work with the system one, so have updated this issue to just be about adding the alpine job to our CI. Does this approach seem reasonable to you?
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3481452455
@github-actions crossbow submit test-r-alpine-linux
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3591600810
@github-actions crossbow submit test-r-alpine-linux
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3591512561
Revision: 22fadf7a31daa2d57b655c56b0e8d859c88e2dea
Submitted crossbow builds: [ursacomputing/crossbow @ actions-f5214c8c49](https://github.com/ursacomputing/crossbow/branches/all?query=actions-f5214c8c49)
|Task|Status|
|----|------|
|test-r-alpine-linux|[](https://github.com/ursacomputing/crossbow/actions/runs/19782176333/job/56683861423)|
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on code in PR #48014:
URL: https://github.com/apache/arrow/pull/48014#discussion_r2616401697
##########
ci/docker/alpine-linux-3.22-r.dockerfile:
##########
@@ -0,0 +1,88 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+# Minimal Alpine Linux container with R for testing Arrow R package
+# on musl libc (CRAN runs checks on Alpine Linux 3.22)
+# Replicates CRAN's Alpine environment as closely as possible
+
+ARG arch=amd64
+FROM ${arch}/alpine:3.22
+
+# Install R and essential build tools
+# Note: bash is needed for Arrow CI scripts, even though CRAN's Alpine uses BusyBox
+RUN apk add \
+ R \
+ R-dev \
+ R-doc \
+ bash \
+ checkbashisms \
+ cmake \
+ curl-dev \
+ g++ \
+ gcc \
+ git \
+ linux-headers \
+ make \
+ musl-locales \
+ openssl-dev \
+ pkgconfig \
+ texlive \
+ texlive-xetex \
+ texmf-dist-fontsextra \
+ texmf-dist-most \
Review Comment:
I'm not saying we should or shouldn't do this, but if I remember correctly we could _not_ build and check the manual and not need to install tex here. Installing tex might not take super long (especially if these are cached), but if that's taking too long, this might help
##########
compose.yaml:
##########
@@ -1774,6 +1775,35 @@ services:
command: >
/bin/bash -c "/arrow/ci/scripts/r_revdepcheck.sh /arrow"
+ alpine-linux-r:
+ # Usage:
+ # docker compose build alpine-linux-r
+ # docker compose run alpine-linux-r
+ # Tests R package installation on musl (Alpine Linux) for CRAN checks.
+ # R package builds C++ from source (bundled RE2 2023-03-01 supports musl).
+ # Parameters:
+ # ALPINE_LINUX: 3.22
+ # R: 4.5 (Alpine's R version)
+ # ARCH: amd64, arm64v8, ...
+ image: ${REPO}:${ARCH}-alpine-linux-${ALPINE_LINUX}-r
+ build:
+ context: .
+ dockerfile: ci/docker/alpine-linux-${ALPINE_LINUX}-r.dockerfile
+ cache_from:
+ - ${REPO}:${ARCH}-alpine-linux-${ALPINE_LINUX}-r
+ args:
+ arch: ${ARCH}
+ shm_size: *shm-size
+ environment:
+ <<: [*common, *sccache]
+ LIBARROW_BINARY: "false"
+ ARROW_SOURCE_HOME: "/arrow"
+ ARROW_R_DEV: "TRUE"
Review Comment:
For some of our other CRAN-like (ubuntu-r-valgrind, r-san, etc) builds we have `ARROW_R_DEV: ${ARROW_R_DEV}` should we follow the same pattern here?
##########
r/src/Makevars.in:
##########
@@ -31,4 +31,4 @@ PKG_LIBS=@libs@
all: $(SHLIB) purify
purify: $(SHLIB)
- @rm -rf ../{libarrow,windows} || true
+ @rm -rf ../libarrow ../windows || true
Review Comment:
Could you say more about this change? I'm a little surprised, but maybe the Alpine shell requires this?
##########
dev/tasks/tasks.yml:
##########
@@ -669,6 +669,13 @@ tasks:
ci: github
template: r/github.linux.cran.yml
+ test-r-alpine-linux-cran:
+ ci: github
+ template: docker-tests/github.linux.yml
+ params:
+ image: alpine-linux-r
+ flags: -e NOT_CRAN=false
Review Comment:
Do we need `NOT_CRAN=false` here at all? It being empty should be the same as being false, but we don't set it elsewhere (And it's not set on CRAN either way). If it is required here, we might have something else up
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic merged PR #48014:
URL: https://github.com/apache/arrow/pull/48014
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3472516612
@github-actions crossbow submit test-r-alpine-linux
Testing the CI job without the nixlibs change first...
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on code in PR #48014:
URL: https://github.com/apache/arrow/pull/48014#discussion_r2626805357
##########
ci/docker/alpine-linux-3.22-r.dockerfile:
##########
@@ -0,0 +1,88 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+# Minimal Alpine Linux container with R for testing Arrow R package
+# on musl libc (CRAN runs checks on Alpine Linux 3.22)
+# Replicates CRAN's Alpine environment as closely as possible
+
+ARG arch=amd64
+FROM ${arch}/alpine:3.22
+
+# Install R and essential build tools
+# Note: bash is needed for Arrow CI scripts, even though CRAN's Alpine uses BusyBox
+RUN apk add \
+ R \
+ R-dev \
+ R-doc \
+ bash \
+ checkbashisms \
+ cmake \
+ curl-dev \
+ g++ \
+ gcc \
+ git \
+ linux-headers \
+ make \
+ musl-locales \
+ openssl-dev \
+ pkgconfig \
+ texlive \
+ texlive-xetex \
+ texmf-dist-fontsextra \
+ texmf-dist-most \
Review Comment:
Thanks both, I've removed these now, and set it to skip the vignettes. These checks should only run as part of the release checks anyway, but good to get them quicker! Good to know re the env var for the font too @bastistician!
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on code in PR #48014:
URL: https://github.com/apache/arrow/pull/48014#discussion_r2626756508
##########
dev/tasks/tasks.yml:
##########
@@ -669,6 +669,13 @@ tasks:
ci: github
template: r/github.linux.cran.yml
+ test-r-alpine-linux-cran:
+ ci: github
+ template: docker-tests/github.linux.yml
+ params:
+ image: alpine-linux-r
+ flags: -e NOT_CRAN=false
Review Comment:
Updated
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3591508537
Revision: 0e3a348accf4366e49387020d950ad6a8f1e75aa
Submitted crossbow builds: [ursacomputing/crossbow @ actions-c2627c1668](https://github.com/ursacomputing/crossbow/branches/all?query=actions-c2627c1668)
|Task|Status|
|----|------|
|test-r-alpine-linux|[](https://github.com/ursacomputing/crossbow/actions/runs/19782100398/job/56683690769)|
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3591519879
Revision: c45e0f78c14cca8c52f92eb41d000d48befd36b2
Submitted crossbow builds: [ursacomputing/crossbow @ actions-70688aa0b2](https://github.com/ursacomputing/crossbow/branches/all?query=actions-70688aa0b2)
|Task|Status|
|----|------|
|test-r-alpine-linux|[](https://github.com/ursacomputing/crossbow/actions/runs/19782295879/job/56684119737)|
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3481704725
Revision: f1daf268fb06608d35816e489b13cabb1d0822fa
Submitted crossbow builds: [ursacomputing/crossbow @ actions-edaae374e2](https://github.com/ursacomputing/crossbow/branches/all?query=actions-edaae374e2)
|Task|Status|
|----|------|
|test-r-alpine-linux|[](https://github.com/ursacomputing/crossbow/actions/runs/19043561659/job/54386237266)|
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3481548813
Revision: ae89e8b451e13902d5ef50ac604c7c871d43e6f7
Submitted crossbow builds: [ursacomputing/crossbow @ actions-2bcbb2c1d0](https://github.com/ursacomputing/crossbow/branches/all?query=actions-2bcbb2c1d0)
|Task|Status|
|----|------|
|test-r-alpine-linux|[](https://github.com/ursacomputing/crossbow/actions/runs/19042563204/job/54382889308)|
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3585670335
Latest failure:
```
/arrow/ci/scripts/r_docker_configure.sh: line 44: apt-get: command not found
```
So next we just need to update that script to use whatever Alpine Linux uses as a package manager
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3596758995
Revision: 6d465be16a781a8c4c2eaa00edcad5eb027bf87d
Submitted crossbow builds: [ursacomputing/crossbow @ actions-339db4ba01](https://github.com/ursacomputing/crossbow/branches/all?query=actions-339db4ba01)
|Task|Status|
|----|------|
|test-r-alpine-linux-cran|[](https://github.com/ursacomputing/crossbow/actions/runs/19825564959/job/56797932183)|
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3596746574
@github-actions crossbow submit test-r-alpine-linux-cran
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3596826450
@github-actions crossbow submit test-r-alpine-linux-cran
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3596880431
Revision: 82c40c07735a0b693d65b44423ae3f95291e0588
Submitted crossbow builds: [ursacomputing/crossbow @ actions-de69a84ec3](https://github.com/ursacomputing/crossbow/branches/all?query=actions-de69a84ec3)
|Task|Status|
|----|------|
|test-r-alpine-linux-cran|[](https://github.com/ursacomputing/crossbow/actions/runs/19826308034/job/56800471296)|
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3619899725
Do we not wanna do R CMD CHECK instead of just running the tests here?
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "nealrichardson (via GitHub)" <gi...@apache.org>.
nealrichardson commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3643681355
> In the R package we use bundled RE2 to build from source, but it doesn't work on Alpine Linux - we should allow system RE2 when building there.
I'm not seeing that in this diff, where does that change of behavior happen?
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on code in PR #48014:
URL: https://github.com/apache/arrow/pull/48014#discussion_r2626748969
##########
compose.yaml:
##########
@@ -1774,6 +1775,35 @@ services:
command: >
/bin/bash -c "/arrow/ci/scripts/r_revdepcheck.sh /arrow"
+ alpine-linux-r:
+ # Usage:
+ # docker compose build alpine-linux-r
+ # docker compose run alpine-linux-r
+ # Tests R package installation on musl (Alpine Linux) for CRAN checks.
+ # R package builds C++ from source (bundled RE2 2023-03-01 supports musl).
+ # Parameters:
+ # ALPINE_LINUX: 3.22
+ # R: 4.5 (Alpine's R version)
+ # ARCH: amd64, arm64v8, ...
+ image: ${REPO}:${ARCH}-alpine-linux-${ALPINE_LINUX}-r
+ build:
+ context: .
+ dockerfile: ci/docker/alpine-linux-${ALPINE_LINUX}-r.dockerfile
+ cache_from:
+ - ${REPO}:${ARCH}-alpine-linux-${ALPINE_LINUX}-r
+ args:
+ arch: ${ARCH}
+ shm_size: *shm-size
+ environment:
+ <<: [*common, *sccache]
+ LIBARROW_BINARY: "false"
+ ARROW_SOURCE_HOME: "/arrow"
+ ARROW_R_DEV: "TRUE"
Review Comment:
Good point; updated.
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3665824107
Revision: 9a816055703d7d72ea64261e40e37ed5b217487b
Submitted crossbow builds: [ursacomputing/crossbow @ actions-4156adbfba](https://github.com/ursacomputing/crossbow/branches/all?query=actions-4156adbfba)
|Task|Status|
|----|------|
|test-r-alpine-linux-cran|[](https://github.com/ursacomputing/crossbow/actions/runs/20307709882/job/58329693253)|
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3666141673
@github-actions crossbow submit test-r-alpine-linux-cran
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3591518664
@github-actions crossbow submit test-r-alpine-linux
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3591652391
@github-actions crossbow submit test-r-alpine-linux-cran
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3481612920
@github-actions crossbow submit test-r-alpine-linux
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3472508752
:warning: GitHub issue #48013 **has been automatically assigned in GitHub** to PR creator.
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3481457886
```
Unable to match any tasks for `test-r-alpine-linux`
The Archery job run can be found at: https://github.com/apache/arrow/actions/runs/19041901360
```
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3591558457
@github-actions crossbow submit test-r-alpine-linux
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "nealrichardson (via GitHub)" <gi...@apache.org>.
nealrichardson commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3646572661
> My bad @nealrichardson, the approach here morphed a bit over time since the original issue that I opened.
>
> Now we have bumped our bundled version of RE2 to be compatible with Alpine in #48011, I don't think we need to work with the system one, so have updated this issue to just be about adding the alpine job to our CI. Does this approach seem reasonable to you?
Makes sense to me! I'll let others weigh in on the specific implementation, this approach seems reasonable to me but I haven't touched crossbow in a long time.
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "bastistician (via GitHub)" <gi...@apache.org>.
bastistician commented on code in PR #48014:
URL: https://github.com/apache/arrow/pull/48014#discussion_r2627596754
##########
ci/scripts/r_test.sh:
##########
@@ -101,7 +101,7 @@ SCRIPT="as_cran <- !identical(tolower(Sys.getenv('NOT_CRAN')), 'true')
build_args <- '--no-build-vignettes'
}
- if (!as_cran && requireNamespace('reticulate', quietly = TRUE) && reticulate::py_module_available('pyarrow')) {
+ if (!as_cran && (requireNamespace('reticulate', quietly = TRUE)) && reticulate::py_module_available('pyarrow')) {
Review Comment:
I don't understand the added parentheses here, they shouldn't make a difference.
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "conbench-apache-arrow[bot] (via GitHub)" <gi...@apache.org>.
conbench-apache-arrow[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3688720456
After merging your PR, Conbench analyzed the 3 benchmarking runs that have been run so far on merge-commit 5de6aa6f15ff798d3b731eebc6855c9190dc0894.
There were no benchmark performance regressions. 🎉
The [full Conbench report](https://github.com/apache/arrow/runs/58849005714) has more details. It also includes information about 20 possible false positives for unstable benchmarks that are known to sometimes produce them.
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3596837523
Revision: bc22b4637f8f1aef7c23e155b32118ee84041c97
Submitted crossbow builds: [ursacomputing/crossbow @ actions-c3d2f3b289](https://github.com/ursacomputing/crossbow/branches/all?query=actions-c3d2f3b289)
|Task|Status|
|----|------|
|test-r-alpine-linux-cran|[](https://github.com/ursacomputing/crossbow/actions/runs/19826086792/job/56799718260)|
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3591507483
@github-actions crossbow submit test-r-alpine-linux
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3595769932
Revision: b1336060dde25a1b67787c7096aeba9d2b6b613b
Submitted crossbow builds: [ursacomputing/crossbow @ actions-1544f46c5c](https://github.com/ursacomputing/crossbow/branches/all?query=actions-1544f46c5c)
|Task|Status|
|----|------|
|test-r-alpine-linux-cran|[](https://github.com/ursacomputing/crossbow/actions/runs/19819329878/job/56777800487)|
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3596215574
Revision: 4153585b772f2a263645b7a1f882548dea73041a
Submitted crossbow builds: [ursacomputing/crossbow @ actions-5a027b6e6a](https://github.com/ursacomputing/crossbow/branches/all?query=actions-5a027b6e6a)
|Task|Status|
|----|------|
|test-r-alpine-linux-cran|[](https://github.com/ursacomputing/crossbow/actions/runs/19822234386/job/56787023505)|
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3472528997
Revision: ab2dbc91728c57107b2739eae5c6a4c94e906e8b
Submitted crossbow builds: [ursacomputing/crossbow @ actions-75a7216cba](https://github.com/ursacomputing/crossbow/branches/all?query=actions-75a7216cba)
|Task|Status|
|----|------|
|test-r-alpine-linux|[](https://github.com/ursacomputing/crossbow/actions/runs/18970500839/job/54176937427)|
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3481684874
@github-actions crossbow submit test-r-alpine-linux
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3591653983
Revision: 528de01270e5306ce83f142b21842e6e105d813b
Submitted crossbow builds: [ursacomputing/crossbow @ actions-eaa0103ba1](https://github.com/ursacomputing/crossbow/branches/all?query=actions-eaa0103ba1)
|Task|Status|
|----|------|
|test-r-alpine-linux-cran|[](https://github.com/ursacomputing/crossbow/actions/runs/19784144202/job/56688280742)|
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Re: [PR] GH-48013: [R] Support R package installation on musl (Alpine Linux) for CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3595760530
@github-actions crossbow submit test-r-alpine-linux-cran
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "bastistician (via GitHub)" <gi...@apache.org>.
bastistician commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3665967881
If you get a segfault when reticulate loads python then this is probably from a known numpy/openblas bug (rstudio/reticulate#1858), which you could work around by setting environment variable `UV_NO_BINARY_PACKAGE=numpy`.
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3666151045
Revision: 5fa4d16832ada83b59901d9bcc080b6b59db2887
Submitted crossbow builds: [ursacomputing/crossbow @ actions-bb37eb6094](https://github.com/ursacomputing/crossbow/branches/all?query=actions-bb37eb6094)
|Task|Status|
|----|------|
|test-r-alpine-linux-cran|[](https://github.com/ursacomputing/crossbow/actions/runs/20309820000/job/58337486337)|
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3666131272
Right, we need to manually set `NOT_CRAN=false` because in `r_test.sh` if it's empty, it gets set to `TRUE`.
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #48014:
URL: https://github.com/apache/arrow/pull/48014#issuecomment-3665705631
@jonkeane So I needed to set `NOT_CRAN` to `FALSE` otherwise it runs the Python tests, not sure exactly why but will have a dig and see if I can work it out.
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "bastistician (via GitHub)" <gi...@apache.org>.
bastistician commented on code in PR #48014:
URL: https://github.com/apache/arrow/pull/48014#discussion_r2623895203
##########
ci/docker/alpine-linux-3.22-r.dockerfile:
##########
@@ -0,0 +1,88 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+# Minimal Alpine Linux container with R for testing Arrow R package
+# on musl libc (CRAN runs checks on Alpine Linux 3.22)
+# Replicates CRAN's Alpine environment as closely as possible
+
+ARG arch=amd64
+FROM ${arch}/alpine:3.22
+
+# Install R and essential build tools
+# Note: bash is needed for Arrow CI scripts, even though CRAN's Alpine uses BusyBox
+RUN apk add \
+ R \
+ R-dev \
+ R-doc \
+ bash \
+ checkbashisms \
+ cmake \
+ curl-dev \
+ g++ \
+ gcc \
+ git \
+ linux-headers \
+ make \
+ musl-locales \
+ openssl-dev \
+ pkgconfig \
+ texlive \
+ texlive-xetex \
+ texmf-dist-fontsextra \
+ texmf-dist-most \
Review Comment:
This is a good point. Especially `texmf-dist-fontsextra` is really big and would only be needed for the `inconsolata` font, which you could avoid via environment variable `R_RD4PDF=times`.
I think you don't need to check building the PDF and HTML manuals in each and every CI run. It should be fine to do this only as part of the release checks. You could use `R CMD check --no-manual --extra-arch` to limit checks to runtime tests in all but one "main" CI configuration.
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Re: [PR] GH-48013: [R] Add CI job for musl (Alpine Linux) to replicate CRAN checks [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on code in PR #48014:
URL: https://github.com/apache/arrow/pull/48014#discussion_r2616479352
##########
r/src/Makevars.in:
##########
@@ -31,4 +31,4 @@ PKG_LIBS=@libs@
all: $(SHLIB) purify
purify: $(SHLIB)
- @rm -rf ../{libarrow,windows} || true
+ @rm -rf ../libarrow ../windows || true
Review Comment:
Ah yeah, should have added a comment; it's a bashism and in Alpine, if bash isn't installed, it fails.
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