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Posted to issues@arrow.apache.org by "amoeba (via GitHub)" <gi...@apache.org> on 2023/03/09 19:54:52 UTC
[GitHub] [arrow] amoeba opened a new issue, #34523: [R] Unable to compile R package with GCS on macOS M1
amoeba opened a new issue, #34523:
URL: https://github.com/apache/arrow/issues/34523
### 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 https://github.com/apache/arrow/issues/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 (2f3f41f05e4bfae24344ee7a4b39ad6719f98751):
<details>
<summary>How I'm building libarrow and the R package</summary>
```
$ 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 .
```
</details>
<details>
<summary>More complete R build output</summary>
```
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’
```
</details>
### Component(s)
R
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[GitHub] [arrow] amoeba commented on issue #34523: [R] Unable to compile R package with GCS on macOS M1
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #34523:
URL: https://github.com/apache/arrow/issues/34523#issuecomment-1533871976
Thanks for the fix @kou !
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[GitHub] [arrow] amoeba commented on issue #34523: [R] Unable to compile R package with GCS on macOS M1
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #34523:
URL: https://github.com/apache/arrow/issues/34523#issuecomment-1462794116
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.
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[GitHub] [arrow] kou commented on issue #34523: [R] Unable to compile R package with GCS on macOS M1
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #34523:
URL: https://github.com/apache/arrow/issues/34523#issuecomment-1531654226
Yes.
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[GitHub] [arrow] kou closed issue #34523: [R] Unable to compile R package with GCS on macOS M1
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou closed issue #34523: [R] Unable to compile R package with GCS on macOS M1
URL: https://github.com/apache/arrow/issues/34523
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[GitHub] [arrow] kou commented on issue #34523: [R] Unable to compile R package with GCS on macOS M1
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #34523:
URL: https://github.com/apache/arrow/issues/34523#issuecomment-1463107903
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.
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[GitHub] [arrow] nealrichardson commented on issue #34523: [R] Unable to compile R package with GCS on macOS M1
Posted by "nealrichardson (via GitHub)" <gi...@apache.org>.
nealrichardson commented on issue #34523:
URL: https://github.com/apache/arrow/issues/34523#issuecomment-1531618756
@kou should we reopen this?
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[GitHub] [arrow] kou commented on issue #34523: [R] Unable to compile R package with GCS on macOS M1
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #34523:
URL: https://github.com/apache/arrow/issues/34523#issuecomment-1463069526
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/`.
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[GitHub] [arrow] amoeba closed issue #34523: [R] Unable to compile R package with GCS on macOS M1
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba closed issue #34523: [R] Unable to compile R package with GCS on macOS M1
URL: https://github.com/apache/arrow/issues/34523
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[GitHub] [arrow] amoeba commented on issue #34523: [R] Unable to compile R package with GCS on macOS M1
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #34523:
URL: https://github.com/apache/arrow/issues/34523#issuecomment-1463098831
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?
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