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Posted to github@arrow.apache.org by "tadeja (via GitHub)" <gi...@apache.org> on 2026/03/10 15:51:12 UTC
[PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
tadeja opened a new pull request, #49491:
URL: https://github.com/apache/arrow/pull/49491
### Rationale for this change
Homebrew upgrading protobuf beyond v33 (as discussed in #49435) also causes a new runtime Bus error.
### What changes are included in this PR?
a) Pin `protobuf@33` in `cpp/Brewfile` (as in #49436)
b) Add keg-only env setup in `python.yml` so CMake/pkg-config can find `protobuf@33`
This resolves `Fatal Python error: Bus error` on macOS 15 Intel when importing `pyarrow.flight`. Homebrew's latest `protobuf` pulls in Abseil 20260107
```-- Found abslAlt: 1 (found version "20260107")```
which is ABI-incompatible with Arrow's bundled gRPC v1.46.3
One of earliest Python CI logs with the `Bus error`:
https://github.com/apache/arrow/actions/runs/22722817262/job/65889451081#step:10:103
Note: Other workflows using `cpp/Brewfile` will prob need similar keg-only setup. (There's [failing C++ job log here](https://github.com/apache/arrow/actions/runs/22892919158/job/66419899798#step:13:492), Ruby etc.)
### Are these changes tested?
Yes, fork workflow completed the Python macOS 15-intel job with success.
### Are there any user-facing changes?
No.
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "raulcd (via GitHub)" <gi...@apache.org>.
raulcd commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4046692807
lol, you beat me to it :)
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "raulcd (via GitHub)" <gi...@apache.org>.
raulcd commented on code in PR #49491:
URL: https://github.com/apache/arrow/pull/49491#discussion_r2924744701
##########
cpp/src/arrow/engine/substrait/options.cc:
##########
@@ -68,17 +68,35 @@ class DefaultExtensionProvider : public BaseExtensionProvider {
const ExtensionSet& ext_set) override {
if (rel.Is<substrait_ext::AsOfJoinRel>()) {
substrait_ext::AsOfJoinRel as_of_join_rel;
+#if PROTOBUF_VERSION >= 3015000
Review Comment:
In the case of `Any.UnpackTo` I don't think the ifdef guard is necessary, I can see that it has been a function that returns a boolean for more than 7 years, just checking really old commits:
https://github.com/protocolbuffers/protobuf/blame/763c3588740b97e8e80b1b1a1a2dc4f417647133/src/google/protobuf/any.pb.h#L119
but we can wait for CI to finish and try to just remove the `ifdef` and just the change as we did for:
`cpp/src/arrow/flight/transport/grpc/serialization_internal.cc`
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Re: [PR] GH-49435: [CI][C++] Fix macOS build with Homebrew protobuf v34 [arrow]
Posted by "conbench-apache-arrow[bot] (via GitHub)" <gi...@apache.org>.
conbench-apache-arrow[bot] commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4050578039
After merging your PR, Conbench analyzed the 3 benchmarking runs that have been run so far on merge-commit 771205b0042b0949ce5fbd24b99211bb36a5dbda.
There were no benchmark performance regressions. 🎉
The [full Conbench report](https://github.com/apache/arrow/runs/66875889718) has more details.
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4033036606
[AMD64 macOS 15-intel Python 3](https://github.com/apache/arrow/actions/runs/22911292559/job/66484148788#logs) and [ARM64 macOS 14 Python 3](https://github.com/apache/arrow/actions/runs/22911292559/job/66484148718#logs) both successfully completed with the protobuf@33 change.
Now attempting similar change for `cpp.yml` and `ruby.yml`.
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Re: [PR] GH-49435: [CI][C++] Fix macOS build with Homebrew protobuf v34 [arrow]
Posted by "raulcd (via GitHub)" <gi...@apache.org>.
raulcd merged PR #49491:
URL: https://github.com/apache/arrow/pull/49491
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on code in PR #49491:
URL: https://github.com/apache/arrow/pull/49491#discussion_r2917309223
##########
.github/workflows/cpp.yml:
##########
@@ -230,6 +230,12 @@ jobs:
brew uninstall pkg-config || :
brew uninstall pkg-config@0.29.2 || :
brew bundle --file=cpp/Brewfile
+
+ # protobuf@33 is keg-only, so make it visible to CMake and pkg-config.
+ export PROTOBUF_PREFIX="$(brew --prefix protobuf@33)"
+ echo "PKG_CONFIG_PATH=${PROTOBUF_PREFIX}/lib/pkgconfig:${PKG_CONFIG_PATH}" >> "$GITHUB_ENV"
+ echo "CMAKE_PREFIX_PATH=${PROTOBUF_PREFIX}:${ARROW_HOME}:${CMAKE_PREFIX_PATH}" >> "$GITHUB_ENV"
+ echo "${PROTOBUF_PREFIX}/bin" >> "$GITHUB_PATH"
Review Comment:
Now there's only [brew "protobuf@33"](https://github.com/apache/arrow/pull/49491/changes#diff-87eb96363e17dbc9cb816c99123f76f25d63eb48920dd785a486ee59ee1997a1R39)
The conditional shouldn't be required - if someone removed workaround of @33 from Brewfile but forgot to update the workflow then failure should happen.
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on code in PR #49491:
URL: https://github.com/apache/arrow/pull/49491#discussion_r2924837429
##########
cpp/src/arrow/engine/substrait/options.cc:
##########
@@ -68,17 +68,35 @@ class DefaultExtensionProvider : public BaseExtensionProvider {
const ExtensionSet& ext_set) override {
if (rel.Is<substrait_ext::AsOfJoinRel>()) {
substrait_ext::AsOfJoinRel as_of_join_rel;
+#if PROTOBUF_VERSION >= 3015000
Review Comment:
[ARM64 macOS 14 Python 3](https://github.com/apache/arrow/actions/runs/23004368281/job/66797009464?pr=49491#logs) and [ARM64 macOS 14 C++](https://github.com/apache/arrow/actions/runs/23004368368/job/66797010466?pr=49491#logs) succeeded!
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "rok (via GitHub)" <gi...@apache.org>.
rok commented on code in PR #49491:
URL: https://github.com/apache/arrow/pull/49491#discussion_r2914000585
##########
.github/workflows/cpp.yml:
##########
@@ -230,6 +230,12 @@ jobs:
brew uninstall pkg-config || :
brew uninstall pkg-config@0.29.2 || :
brew bundle --file=cpp/Brewfile
+
+ # protobuf@33 is keg-only, so make it visible to CMake and pkg-config.
+ export PROTOBUF_PREFIX="$(brew --prefix protobuf@33)"
+ echo "PKG_CONFIG_PATH=${PROTOBUF_PREFIX}/lib/pkgconfig:${PKG_CONFIG_PATH}" >> "$GITHUB_ENV"
+ echo "CMAKE_PREFIX_PATH=${PROTOBUF_PREFIX}:${ARROW_HOME}:${CMAKE_PREFIX_PATH}" >> "$GITHUB_ENV"
+ echo "${PROTOBUF_PREFIX}/bin" >> "$GITHUB_PATH"
Review Comment:
Perhaps this could be conditional to protobuf@33? [Like here](https://github.com/gazebo-tooling/release-tools/pull/1454/changes).
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Re: [PR] GH-49435: [CI][C++] Fix macOS build with Homebrew protobuf v34 [arrow]
Posted by "raulcd (via GitHub)" <gi...@apache.org>.
raulcd commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4047456448
@tadeja can you update the description of the PR to describe the current changes? I am happy to merge after that
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4038527857
Ruby job is failing anew (no changes here except for newline)
https://github.com/apache/arrow/actions/runs/22944683842/job/66602842927?pr=49491#step:8:1689
```/Users/runner/work/arrow/arrow/build/cpp/src/arrow/flight/Flight.pb.h:16:2: error: "Protobuf C++ gencode is built with an incompatible version of"```
I see [homebrew merged this](https://github.com/Homebrew/homebrew-core/pull/270395) last night so grpc changed "protobuf@33" to "protobuf" and is on version 34.0 now;
- https://github.com/Homebrew/homebrew-core/commit/552efcaee029b5da432f2a9ef93c0db90aed1b17#diff-1bd6970eef0fe40eabd3ee6d2f57b3dfec00fc5579e0a13856c45a0381082150R37
- https://formulae.brew.sh/formula/grpc
As it appears grpc formula now depends on protobuf (v34), grpc_cpp_plugin generates v34 incompatible code that can't compile against protobuf@33 headers
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4033379160
@raulcd, @rok what do you say about this PR? it can be moved into existing draft #49436 if you'd prefer.
+ unrelated job 'test_write_dataset_s3_put_only' timeout failure could use a re-run: https://github.com/apache/arrow/actions/runs/22914401035/job/66495531287?pr=49491#step:10:266
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on code in PR #49491:
URL: https://github.com/apache/arrow/pull/49491#discussion_r2924078810
##########
.github/workflows/cpp.yml:
##########
@@ -230,6 +230,15 @@ jobs:
brew uninstall pkg-config || :
brew uninstall pkg-config@0.29.2 || :
brew bundle --file=cpp/Brewfile
+
+ # protobuf@33 is keg-only, so make it visible to CMake and pkg-config.
+ # Remove this workaround after the gRPC problem is fixed.
+ # See https://github.com/grpc/grpc/issues/41755
+ export PROTOBUF_PREFIX="$(brew --prefix protobuf@33)"
+ echo "PKG_CONFIG_PATH=${PROTOBUF_PREFIX}/lib/pkgconfig:${PKG_CONFIG_PATH}" >> "$GITHUB_ENV"
+ echo "CMAKE_PREFIX_PATH=${PROTOBUF_PREFIX}:${ARROW_HOME}:${CMAKE_PREFIX_PATH}" >> "$GITHUB_ENV"
+ echo "${PROTOBUF_PREFIX}/bin" >> "$GITHUB_PATH"
Review Comment:
Good, I am changing this to `brew update`!
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on code in PR #49491:
URL: https://github.com/apache/arrow/pull/49491#discussion_r2915266041
##########
.github/workflows/ruby.yml:
##########
@@ -162,6 +162,12 @@ jobs:
brew update
brew bundle --file=cpp/Brewfile
brew bundle --file=c_glib/Brewfile
+
+ # protobuf@33 is keg-only, so make it visible to CMake and pkg-config.
+ export PROTOBUF_PREFIX="$(brew --prefix protobuf@33)"
+ echo "PKG_CONFIG_PATH=${PROTOBUF_PREFIX}/lib/pkgconfig:${PKG_CONFIG_PATH}" >> "$GITHUB_ENV"
+ echo "CMAKE_PREFIX_PATH=${PROTOBUF_PREFIX}:${ARROW_HOME}:${CMAKE_PREFIX_PATH}" >> "$GITHUB_ENV"
+ echo "${PROTOBUF_PREFIX}/bin" >> "$GITHUB_PATH"
Review Comment:
```suggestion
echo "${PROTOBUF_PREFIX}/bin" >> "$GITHUB_PATH"
```
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Re: [PR] GH-49435: [CI][C++] Fix macOS build with Homebrew protobuf v34 [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4047653908
Hopefully this is it for a while. Thank you @kou and @raulcd !
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on code in PR #49491:
URL: https://github.com/apache/arrow/pull/49491#discussion_r2922522159
##########
.github/workflows/cpp.yml:
##########
@@ -230,6 +230,15 @@ jobs:
brew uninstall pkg-config || :
brew uninstall pkg-config@0.29.2 || :
brew bundle --file=cpp/Brewfile
+
+ # protobuf@33 is keg-only, so make it visible to CMake and pkg-config.
+ # Remove this workaround after the gRPC problem is fixed.
+ # See https://github.com/grpc/grpc/issues/41755
+ export PROTOBUF_PREFIX="$(brew --prefix protobuf@33)"
+ echo "PKG_CONFIG_PATH=${PROTOBUF_PREFIX}/lib/pkgconfig:${PKG_CONFIG_PATH}" >> "$GITHUB_ENV"
+ echo "CMAKE_PREFIX_PATH=${PROTOBUF_PREFIX}:${ARROW_HOME}:${CMAKE_PREFIX_PATH}" >> "$GITHUB_ENV"
+ echo "${PROTOBUF_PREFIX}/bin" >> "$GITHUB_PATH"
Review Comment:
Can we use `brew update` workaround instead of this?
We can remove the `brew update` once GitHub Actions runner ships new Homebrew by default.
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "raulcd (via GitHub)" <gi...@apache.org>.
raulcd commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4046690383
@tadeja can you try applying the following:
```diff
$ git diff
diff --git a/cpp/src/arrow/engine/substrait/expression_internal.cc b/cpp/src/arrow/engine/substrait/expression_internal.cc
index d91edbfce6..8ad7c93780 100644
--- a/cpp/src/arrow/engine/substrait/expression_internal.cc
+++ b/cpp/src/arrow/engine/substrait/expression_internal.cc
@@ -804,7 +804,13 @@ struct ScalarToProtoImpl {
auto user_defined = std::make_unique<Lit::UserDefined>();
user_defined->set_type_reference(anchor);
auto value_any = std::make_unique<google::protobuf::Any>();
+#if PROTOBUF_VERSION >= 3015000
+ if (!value_any.PackFrom(value)) {
+ return Status::IOError("Failed to pack user defined value");
+ }
+#else
value_any->PackFrom(value);
+#endif
user_defined->set_allocated_value(value_any.release());
lit_->set_allocated_user_defined(user_defined.release());
return Status::OK();
```
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4046775113
Ok, @raulcd it's indeed now failing at options.cc too, I am adding similar if-else
https://github.com/apache/arrow/actions/runs/23003764617/job/66794807259#step:9:1956
https://github.com/apache/arrow/actions/runs/23003764691/job/66794807733#step:12:2438
```
[808/1314] Building CXX object src/arrow/engine/CMakeFiles/arrow_substrait_objlib.dir/substrait/options.cc.o
FAILED: [code=1] src/arrow/engine/CMakeFiles/arrow_substrait_objlib.dir/substrait/options.cc.o
< ... >
/Users/runner/work/arrow/arrow/cpp/src/arrow/engine/substrait/options.cc:71:7: error: ignoring return value of function declared with 'nodiscard' attribute [-Werror,-Wunused-result]
rel.UnpackTo(&as_of_join_rel);
^~~~~~~~~~~~ ~~~~~~~~~~~~~~~
```
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on code in PR #49491:
URL: https://github.com/apache/arrow/pull/49491#discussion_r2924822540
##########
cpp/src/arrow/engine/substrait/options.cc:
##########
@@ -68,17 +68,35 @@ class DefaultExtensionProvider : public BaseExtensionProvider {
const ExtensionSet& ext_set) override {
if (rel.Is<substrait_ext::AsOfJoinRel>()) {
substrait_ext::AsOfJoinRel as_of_join_rel;
+#if PROTOBUF_VERSION >= 3015000
Review Comment:
ah, Ok, let me redo that.
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4039200151
( Unrelated issue of [Windows test segfault](https://github.com/apache/arrow/actions/runs/22953079664/job/66622464305?pr=49491#step:12:341) is being worked on in #49462. )
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "rok (via GitHub)" <gi...@apache.org>.
rok commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4033895287
Will users building for source need to use keg only? Should we update docs?
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4040435259
@raulcd what are your thoughts on the next steps here? - CI jobs are passing again today, also for [ARM64 macOS 14 GLib & Ruby (pull_request)](https://github.com/apache/arrow/actions/runs/22959190132/job/66644607657?pr=49491)
This time using solution [from your draft PR](https://github.com/apache/arrow/pull/49436/changes#diff-d00bf1f12f09f139f79a7fd12da91320a444356a298a6bb9d315869f277d7d79R540-R546) + protobuf@33 workaround *only for* cpp.yml and python.yml + reverted env setup for ruby.yml as that doesn't seem to be necessary there anymore [I suppose due to brew update last night](https://github.com/apache/arrow/pull/49491#issuecomment-4038527857)? (I'll remove [unneeded newline ](https://github.com/apache/arrow/pull/49491/changes#diff-ce0dee93a528f6c7648f4cd671a3ec7be6a80f976c88f3aa1c322b7a80828fbaR165) with my next commit)
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Re: [PR] GH-49435: [CI][Python] Fix macOS protobuf@33 keg-only discovery [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on PR #49491:
URL: https://github.com/apache/arrow/pull/49491#issuecomment-4046620687
With only `brew update` approach now [ARM64 macOS 14 Python 3](https://github.com/apache/arrow/actions/runs/23001468652/job/66786911071#step:9:1950) failing at
```
[586/661] Building CXX object src/arrow/engine/CMakeFiles/arrow_substrait_objlib.dir/substrait/expression_internal.cc.o
FAILED: [code=1] src/arrow/engine/CMakeFiles/arrow_substrait_objlib.dir/substrait/expression_internal.cc.o
/opt/homebrew/bin/ccache /usr/bin/c++ -DARROW< ... >
/Users/runner/work/arrow/arrow/cpp/src/arrow/engine/substrait/expression_internal.cc:807:5: error: ignoring return value of function declared with 'nodiscard' attribute [-Werror,-Wunused-result]
value_any->PackFrom(value);
^~~~~~~~~~~~~~~~~~~ ~~~~~
1 error generated.
```
and [ARM64 macOS 14 C++](https://github.com/apache/arrow/actions/runs/23001468779/job/66786881243#step:12:2444) at
```
[808/1314] Building CXX object src/arrow/engine/CMakeFiles/arrow_substrait_objlib.dir/substrait/expression_internal.cc.o
FAILED: [code=1] src/arrow/engine/CMakeFiles/arrow_substrait_objlib.dir/substrait/expression_internal.cc.o
< ... >
/Users/runner/work/arrow/arrow/cpp/src/arrow/engine/substrait/expression_internal.cc:807:5: error: ignoring return value of function declared with 'nodiscard' attribute [-Werror,-Wunused-result]
value_any->PackFrom(value);
^~~~~~~~~~~~~~~~~~~ ~~~~~
1 error generated.
```
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Re: [PR] GH-49435: [CI][C++] Fix macOS build with Homebrew protobuf v34 [arrow]
Posted by "tadeja (via GitHub)" <gi...@apache.org>.
tadeja commented on code in PR #49491:
URL: https://github.com/apache/arrow/pull/49491#discussion_r2925263608
##########
cpp/src/arrow/engine/substrait/options.cc:
##########
@@ -68,17 +68,35 @@ class DefaultExtensionProvider : public BaseExtensionProvider {
const ExtensionSet& ext_set) override {
if (rel.Is<substrait_ext::AsOfJoinRel>()) {
substrait_ext::AsOfJoinRel as_of_join_rel;
+#if PROTOBUF_VERSION >= 3015000
Review Comment:
@raulcd this is redone and CI all green again.
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