GH-50609: [CI][Dev] Fix shellcheck errors in the ci/scripts/r_deps.sh by hiroyuki-sato · Pull Request #50610 · apache/arrow

hiroyuki-sato · 2026-07-23T00:42:22Z

Rationale for this change

This is the sub issue #44748.

SC2027: The surrounding quotes actually unquote this. Remove or escape them.
SC2086: Double quote to prevent globbing and word splitting.
SC2223: This default assignment may cause DoS due to globbing. Quote it.

shellcheck ci/scripts/r_deps.sh

In ci/scripts/r_deps.sh line 21:
: ${R_BIN:=R}
  ^---------^ SC2223 (info): This default assignment may cause DoS due to globbing. Quote it.


In ci/scripts/r_deps.sh line 23:
: ${R_PRUNE_DEPS:=FALSE}
  ^--------------------^ SC2223 (info): This default assignment may cause DoS due to globbing. Quote it.


In ci/scripts/r_deps.sh line 24:
R_PRUNE_DEPS=`echo $R_PRUNE_DEPS | tr '[:upper:]' '[:lower:]'`
             ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.
                   ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean:
R_PRUNE_DEPS=$(echo "$R_PRUNE_DEPS" | tr '[:upper:]' '[:lower:]')


In ci/scripts/r_deps.sh line 26:
: ${R_DUCKDB_DEV:=FALSE}
  ^--------------------^ SC2223 (info): This default assignment may cause DoS due to globbing. Quote it.


In ci/scripts/r_deps.sh line 27:
R_DUCKDB_DEV=`echo $R_DUCKDB_DEV | tr '[:upper:]' '[:lower:]'`
             ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.
                   ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean:
R_DUCKDB_DEV=$(echo "$R_DUCKDB_DEV" | tr '[:upper:]' '[:lower:]')


In ci/scripts/r_deps.sh line 31:
pushd ${source_dir}
      ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean:
pushd "${source_dir}"


In ci/scripts/r_deps.sh line 33:
if [ ${R_PRUNE_DEPS} = "true" ]; then
     ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean:
if [ "${R_PRUNE_DEPS}" = "true" ]; then


In ci/scripts/r_deps.sh line 46:
${R_BIN} -e "options(warn=2); install.packages('remotes'); remotes::install_cran(c('glue', 'rcmdcheck', 'sys')); remotes::install_deps(INSTALL_opts = '"${INSTALL_ARGS}"')"
                                                                                                                                                        ^-------------^ SC2027 (warning): The surrounding quotes actually unquote this. Remove or escape them.
                                                                                                                                                        ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean:
${R_BIN} -e "options(warn=2); install.packages('remotes'); remotes::install_cran(c('glue', 'rcmdcheck', 'sys')); remotes::install_deps(INSTALL_opts = '""${INSTALL_ARGS}""')"


In ci/scripts/r_deps.sh line 49:
if [ ${R_DUCKDB_DEV} == "true" ]; then
     ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean:
if [ "${R_DUCKDB_DEV}" == "true" ]; then


In ci/scripts/r_deps.sh line 55:
${R_BIN} -e "remotes::install_deps(dependencies = TRUE, INSTALL_opts = '"${INSTALL_ARGS}"')"
                                                                         ^-------------^ SC2027 (warning): The surrounding quotes actually unquote this. Remove or escape them.
                                                                         ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean:
${R_BIN} -e "remotes::install_deps(dependencies = TRUE, INSTALL_opts = '""${INSTALL_ARGS}""')"

For more information:
  https://www.shellcheck.net/wiki/SC2027 -- The surrounding quotes actually u...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2223 -- This default assignment may cause...

What changes are included in this PR?

SC2027: Remove redundant quotes.
SC2086: Quote variable expansions.
SC2223: Quote default variable assignments.

Are these changes tested?

Yes.

Are there any user-facing changes?

No.

GitHub Issue: [CI][Dev] Fix shellcheck errors in the ci/scripts/r_deps.sh #50609

github-actions · 2026-07-23T00:42:48Z

⚠️ GitHub issue #50609 has been automatically assigned in GitHub to PR creator.

kou · 2026-07-23T02:31:42Z

@github-actions crossbow submit -g r

github-actions · 2026-07-23T02:34:55Z

Revision: 48a4a03

Submitted crossbow builds: ursacomputing/crossbow @ actions-a93615c8b7

Task	Status
r-binary-packages
r-recheck-most
test-r-alpine-linux-cran
test-r-arrow-backwards-compatibility
test-r-depsource-system
test-r-dev-duckdb
test-r-devdocs
test-r-extra-packages
test-r-fedora-clang
test-r-gcc-11
test-r-gcc-12
test-r-install-local
test-r-install-local-minsizerel
test-r-linux-as-cran
test-r-linux-rchk
test-r-linux-sanitizers
test-r-linux-valgrind
test-r-m1-san
test-r-macos-as-cran
test-r-offline-maximal
test-r-ubuntu-22.04
test-r-versions
test-r-wasm

hiroyuki-sato · 2026-07-23T06:38:59Z

@github-actions crossbow submit -g r

github-actions · 2026-07-23T06:42:14Z

Revision: 85f2b3e

Submitted crossbow builds: ursacomputing/crossbow @ actions-47fe7ddf85

Task	Status
r-binary-packages
r-recheck-most
test-r-alpine-linux-cran
test-r-arrow-backwards-compatibility
test-r-depsource-system
test-r-dev-duckdb
test-r-devdocs
test-r-extra-packages
test-r-fedora-clang
test-r-gcc-11
test-r-gcc-12
test-r-install-local
test-r-install-local-minsizerel
test-r-linux-as-cran
test-r-linux-rchk
test-r-linux-sanitizers
test-r-linux-valgrind
test-r-m1-san
test-r-macos-as-cran
test-r-offline-maximal
test-r-ubuntu-22.04
test-r-versions
test-r-wasm

kou · 2026-07-24T02:20:32Z

Let's wait for #50587 before we merge this because the current R related CI jobs are broken.

hiroyuki-sato · 2026-07-24T08:28:09Z

Thanks I got it.

hiroyuki-sato · 2026-07-24T12:31:42Z

Since #47404 also modifies .pre-commit-config.yaml, there may be a merge conflict if either PR is merged first. If that happens, I'll rebase this PR again.

hiroyuki-sato · 2026-07-24T12:36:15Z

#47404 has been merged, so I rebased this PR.

hiroyuki-sato · 2026-07-24T12:38:16Z

@github-actions crossbow submit -g r

raulcd · 2026-07-24T12:38:38Z

    hooks:
      - id: shellcheck
        alias: shell
        # TODO: Remove this when we fix all lint failures


from my understanding we are close to having this. Is the idea to have a follow up and remove this list afterwards. I am unsure if there has been new shell scripts created since this list was built.

@raulcd

Once I fix the remaining six files in ci/scripts, we should be able to remove that part.

ci/scripts/r_docker_configure.sh: SC2006 SC2046 SC2086 SC2223

ci/scripts/r_install_system_dependencies.sh: SC2006 SC2223

ci/scripts/r_sanitize.sh: SC2086 SC2155 SC2223

ci/scripts/r_test.sh: SC1091 SC2086 SC2223

ci/scripts/r_valgrind.sh: SC2046 SC2086 SC2223

ci/scripts/r_windows_build.sh: SC2011 SC2034 SC2035 SC2046 SC2086 SC2155 SC2223

We’re almost there 😄

github-actions · 2026-07-24T12:41:28Z

Revision: fab7f57

Submitted crossbow builds: ursacomputing/crossbow @ actions-bc2d28fb9f

Task	Status
r-binary-packages
r-recheck-most
test-r-alpine-linux-cran
test-r-arrow-backwards-compatibility
test-r-depsource-system
test-r-dev-duckdb
test-r-devdocs
test-r-extra-packages
test-r-fedora-clang
test-r-gcc-11
test-r-gcc-12
test-r-install-local
test-r-install-local-minsizerel
test-r-linux-as-cran
test-r-linux-rchk
test-r-linux-sanitizers
test-r-linux-valgrind
test-r-m1-san
test-r-macos-as-cran
test-r-offline-maximal
test-r-ubuntu-22.04
test-r-versions
test-r-wasm

hiroyuki-sato · 2026-07-24T14:07:35Z

Is the failure of the Python / AMD64 macOS 15-intel Python 3 (pull_request) CI job related to this PR?

It passed before the rebase, so I suspect the failure may be unrelated to this PR.

https://github.com/apache/arrow/actions/runs/30093588302/job/89482235673?pr=50610#step:11:210

=================================== FAILURES ===================================
________________________ test_write_dataset_s3_put_only ________________________
[gw0] darwin -- Python 3.11.9 /Library/Frameworks/Python.framework/Versions/3.11/bin/python

s3_server = {'connection': ('127.0.0.1', 49384, 'arrow', 'apachearrow'), 'process': <Popen: returncode: None args: ['minio', '--co......>, 'tempdir': local('/private/var/folders/8j/3c4g2vh16vgc8j40cj25qfqh0000gn/T/pytest-of-runner/pytest-0/popen-gw0')}

    @pytest.mark.parquet
    @pytest.mark.s3
    def test_write_dataset_s3_put_only(s3_server):
        # [ARROW-15892] Testing the create_dir flag which will restrict
        # creating a new directory for writing a dataset. This is
        # required while writing a dataset in s3 where we have very
        # limited permissions and thus we can directly write the dataset
        # without creating a directory.
        from pyarrow.fs import S3FileSystem
    
        # write dataset with s3 filesystem
        host, port, _, _ = s3_server['connection']
    
>       _configure_s3_limited_user(s3_server, _minio_put_only_policy,
                                   'test_dataset_limited_user', 'limited123')

/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/pyarrow/tests/test_dataset.py:5206: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/pyarrow/tests/util.py:417: in _configure_s3_limited_user
    _run_mc_command(mcdir, 'admin', 'policy', 'attach',
/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/pyarrow/tests/util.py:366: in _run_mc_command
    retval = proc.wait(10)
             ^^^^^^^^^^^^^
/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py:1264: in wait
    return self._wait(timeout=timeout)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <Popen: returncode: -13 args: ['mc', '-C', '/private/var/folders/8j/3c4g2vh1...>
timeout = 10

    def _wait(self, timeout):
        """Internal implementation of wait() on POSIX."""
        if self.returncode is not None:
            return self.returncode
    
        if timeout is not None:
            endtime = _time() + timeout
            # Enter a busy loop if we have a timeout.  This busy loop was
            # cribbed from Lib/threading.py in Thread.wait() at r71065.
            delay = 0.0005 # 500 us -> initial delay of 1 ms
            while True:
                if self._waitpid_lock.acquire(False):
                    try:
                        if self.returncode is not None:
                            break  # Another thread waited.
                        (pid, sts) = self._try_wait(os.WNOHANG)
                        assert pid == self.pid or pid == 0
                        if pid == self.pid:
                            self._handle_exitstatus(sts)
                            break
                    finally:
                        self._waitpid_lock.release()
                remaining = self._remaining_time(endtime)
                if remaining <= 0:
>                   raise TimeoutExpired(self.args, timeout)
E                   subprocess.TimeoutExpired: Command '['mc', '-C', '/private/var/folders/8j/3c4g2vh16vgc8j40cj25qfqh0000gn/T/pytest-of-runner/pytest-0/popen-gw0/mc', 'admin', 'policy', 'attach', 'myminio/', 'no-create-buckets', '--user', 'test_dataset_limited_user']' timed out after 10 seconds

/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py:2045: TimeoutExpired
----------------------------- Captured stdout call -----------------------------
Cmd: mc -C /private/var/folders/8j/3c4g2vh16vgc8j40cj25qfqh0000gn/T/pytest-of-runner/pytest-0/popen-gw0/mc alias set myminio http://127.0.0.1:49384/ arrow apachearrow
  Return: 0
  Stdout: Added `myminio` successfully.

  Stderr: 
Cmd: mc -C /private/var/folders/8j/3c4g2vh16vgc8j40cj25qfqh0000gn/T/pytest-of-runner/pytest-0/popen-gw0/mc admin user add myminio/ test_dataset_limited_user limited123
  Return: 0
  Stdout: Added user `test_dataset_limited_user` successfully.

  Stderr: 
Cmd: mc -C /private/var/folders/8j/3c4g2vh16vgc8j40cj25qfqh0000gn/T/pytest-of-runner/pytest-0/popen-gw0/mc admin policy create myminio/ no-create-buckets /private/var/folders/8j/3c4g2vh16vgc8j40cj25qfqh0000gn/T/pytest-of-runner/pytest-0/popen-gw0/limited-buckets-policy.json
  Return: 0
  Stdout: Created policy `no-create-buckets` successfully.

  Stderr: 
=============================== warnings summary ===============================

raulcd · 2026-07-24T16:20:06Z

Error is unrelated, is a flaky timeout with minio:

 >                   raise TimeoutExpired(self.args, timeout)
E                   subprocess.TimeoutExpired: Command '['mc', '-C', '/private/var/folders/8j/3c4g2vh16vgc8j40cj25qfqh0000gn/T/pytest-of-runner/pytest-0/popen-gw0/mc', 'admin', 'policy', 'attach', 'myminio/', 'no-create-buckets', '--user', 'test_dataset_limited_user']' timed out after 10 seconds

/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py:2045: TimeoutExpired

kou · 2026-07-24T21:51:52Z

Could you rebase again for #50587?

…eps.sh

Co-authored-by: Sutou Kouhei <kou@cozmixng.org>

…eps.sh

hiroyuki-sato · 2026-07-24T23:39:12Z

@github-actions crossbow submit -g r

hiroyuki-sato · 2026-07-24T23:39:47Z

@kou @raulcd Thank you for your comment. rebased

github-actions · 2026-07-24T23:42:16Z

Revision: 11523fd

Submitted crossbow builds: ursacomputing/crossbow @ actions-b355b52d7d

Task	Status
r-binary-packages
r-recheck-most
test-r-alpine-linux-cran
test-r-arrow-backwards-compatibility
test-r-depsource-system
test-r-dev-duckdb
test-r-devdocs
test-r-extra-packages
test-r-fedora-clang
test-r-gcc-11
test-r-gcc-12
test-r-install-local
test-r-install-local-minsizerel
test-r-linux-as-cran
test-r-linux-rchk
test-r-linux-sanitizers
test-r-linux-valgrind
test-r-m1-san
test-r-macos-as-cran
test-r-offline-maximal
test-r-ubuntu-22.04
test-r-versions
test-r-wasm

hiroyuki-sato requested review from assignUser, jonkeane, kou and raulcd as code owners July 23, 2026 00:42

github-actions Bot added the awaiting review Awaiting review label Jul 23, 2026

kou added the CI: Extra: R Run extra R CI label Jul 23, 2026

kou reviewed Jul 23, 2026

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hiroyuki-sato mentioned this pull request Jul 24, 2026

GH-47402: [CI][Dev] Fix shellcheck errors in the ci/scripts/python_test_emscripten.sh #47403

Merged

hiroyuki-sato force-pushed the topic/shellcheck-r_deps branch from 85f2b3e to fab7f57 Compare July 24, 2026 12:34

github-actions Bot added awaiting change review Awaiting change review and removed awaiting changes Awaiting changes labels Jul 24, 2026

raulcd reviewed Jul 24, 2026

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hiroyuki-sato and others added 4 commits July 25, 2026 08:37

apacheGH-50609: [CI][Dev] Fix shellcheck errors in the ci/scripts/r_d…

a19f1ac

…eps.sh

Update ci/scripts/r_deps.sh

14baacb

Co-authored-by: Sutou Kouhei <kou@cozmixng.org>

apacheGH-50609: [CI][Dev] Fix shellcheck errors in the ci/scripts/r_d…

0287bbd

…eps.sh

apacheGH-50609: [CI][Dev] Fix shellcheck errors in the ci/scripts/r_d…

11523fd

…eps.sh

hiroyuki-sato force-pushed the topic/shellcheck-r_deps branch from fab7f57 to 11523fd Compare July 24, 2026 23:37

github-actions Bot added awaiting change review Awaiting change review and removed awaiting changes Awaiting changes labels Jul 24, 2026

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