[R] Unable to compile R package with GCS on macOS M1

[amoeba]

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

I'm encountering an issue when trying to build the R package from a local build of Arrow C++ but only when I have GCS enabled. The error happens when I run R CMD INSTALL --preclean --no-multiarch .:

symbol not found in flat namespace '__ZN4absl12lts_2023012510FormatTimeENSt3__117basic_string_viewIcNS1_11char_traitsIcEEEENS0_4TimeENS0_8TimeZoneE

This looked very similar to what was reported in #32487, though I'm not building tests. I first tried setting CMAKE_CXX_STANDARD=17 which didn't help. @nealrichardson recommended absl_SOURCE=BUNDLED which also didn't help. I do have abseil via Homebrew.

I'm including some details of how I'm building everything below. I'm building off of main (2f3f41f):

How I'm building libarrow and the R package

$ echo $ARROW_HOME
/Users/bryce/builds/arrow-arm64

$ pwd
/Users/bryce/src/apache/arrow/cpp/build

$ cmake .. \
      -GNinja \
      -DARROW_COMPUTE=ON \
      -DARROW_CSV=ON \
      -DARROW_DATASET=ON \
      -DARROW_FILESYSTEM=ON \
      -DARROW_JSON=ON \
      -DARROW_PARQUET=ON \
      -DARROW_INSTALL_NAME_RPATH=OFF \
      -DARROW_S3=ON \
      -DARROW_GCS=ON \
      -DARROW_MIMALLOC=OFF \
      -DARROW_WITH_BROTLI=ON \
      -DARROW_WITH_BZ2=ON \
      -DARROW_WITH_LZ4=ON \
      -DARROW_WITH_SNAPPY=ON \
      -DARROW_WITH_ZLIB=ON \
      -DARROW_WITH_ZSTD=ON \
      -DARROW_EXTRA_ERROR_CONTEXT=ON \
      -DCMAKE_INSTALL_PREFIX=$ARROW_HOME \
      -DCMAKE_BUILD_TYPE=Release \
      -DGTest_SOURCE=BUNDLED \
      -DCMAKE_CXX_STANDARD=17 \
      -Dabsl_SOURCE=BUNDLED

$ ninja install
$ cd ~/src/apache/arrow/r
$ R CMD INSTALL --preclean --no-multiarch .

More complete R build output

installing to /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-r/00new/arrow/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘arrow’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-r/00new/arrow/libs/arrow.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-r/00new/arrow/libs/arrow.so, 0x0006): symbol not found in flat namespace '__ZN4absl12lts_2023012510FormatTimeENSt3__117basic_string_viewIcNS1_11char_traitsIcEEEENS0_4TimeENS0_8TimeZoneE'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/arrow’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/arrow’

Component(s)

R

[amoeba]

Removing Homebrew abseil then re-building from scratch worked. I was then able to reinstall abseil from Homebrew and build w/o absl_SOURCE=BUNDLED which is what I had been doing before I ran into this. So I'm not sure what state I had gotten my system into to run into this in the first place.

[kou]

Ah, this is caused by mixing include paths.
Some dependencies installed by Homebrew add -I$(brew --prefix)/include and it may be used before bundled Abseil. It mixes Homebrew Abseil's include/ and bundled Abseil's lib/.

[amoeba]

Interesting @kou, thanks. This is an area I'm not very familiar with but is there a possibility for an improvement to the build system here?

[kou]

CMake has some features to control include path order. For example, target_include_directories() https://cmake.org/cmake/help/latest/command/target_include_directories.html provides AFTER/BEFORE.

We may be able to solve this by these features.

[nealrichardson]

@kou should we reopen this?

[kou]

Yes.

[amoeba]

Thanks for the fix @kou !