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[CI][C++] Emscripten nightly jobs fail at CMake configure for Protobuf #55380

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@tadeja

Describe the bug, including details regarding any error messages, version, and platform.

Nightly jobs
test-conda-python-emscripten and test-ubuntu-22.04-cpp-emscripten have been failing the last 8 at -- Protobuf: Building Protocol Buffers from source using FetchContent
https://github.com/ursacomputing/crossbow/actions/runs/41397083958/job/125120623586

https://github.com/ursacomputing/crossbow/actions/runs/41397099985/job/125120673162#step:7:733

Protobuf: [3/9] Performing patch step for 'protobuf-populate'
Protobuf: patching file src/google/protobuf/port_def.inc
Protobuf: Hunk #1 FAILED at 435.
Protobuf: 1 out of 1 hunk FAILED -- saving rejects to file src/google/protobuf/port_def.inc.rej
Protobuf: FAILED: protobuf-populate-prefix/src/protobuf-populate-stamp/protobuf-populate-patch /build/cpp/_deps/protobuf-subbuild/protobuf-populate-prefix/src/protobuf-populate-stamp/protobuf-populate-patch 
Protobuf: cd /build/cpp/_deps/protobuf-src && /usr/bin/patch -p1 -i /arrow/cpp/cmake_modules/protobuf-emscripten.patch && /usr/local/bin/cmake -E touch /build/cpp/_deps/protobuf-subbuild/protobuf-populate-prefix/src/protobuf-populate-stamp/protobuf-populate-patch
Protobuf: ninja: build stopped: subcommand failed.
Protobuf: 
CMake Error at /usr/local/share/cmake-3.26/Modules/FetchContent.cmake:1622 (message):
  Build step for protobuf failed: 1

THe protobuf-emscripten.patch got first created for protobuf 31.1 with #48926 / PR #48964,
now recent #54927 bumped protobuf from 31.1 to 36.2 and Emscripten protobuf patch doesn't seem to apply anymore.

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Continuous Integration, C++

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