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Posted to issues@arrow.apache.org by "barracuda156 (via GitHub)" <gi...@apache.org> on 2023/11/17 21:18:32 UTC
[I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
barracuda156 opened a new issue, #38769:
URL: https://github.com/apache/arrow/issues/38769
### Describe the bug, including details regarding any error messages, version, and platform.
I wanted to update `arrow` in Macports now, but linking of `R-arrow` 14.0.0 (what CRAN has released) fails for me against `arrow` 14.0.1:
```
/opt/local/bin/g++-mp-13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/Library/Frameworks/R.framework/Resources/lib -Wl,-headerpad_max_install_names -Wl,-rpath,/opt/local/lib/libgcc -L/opt/local/lib -lMacportsLegacySupport -arch ppc -o arrow.so RTasks.o altrep.o array.o array_to_vector.o arraydata.o arrowExports.o bridge.o buffer.o chunkedarray.o compression.o compute-exec.o compute.o config.o csv.o dataset.o datatype.o expression.o extension-impl.o feather.o field.o filesystem.o io.o json.o memorypool.o message.o parquet.o r_to_arrow.o recordbatch.o recordbatchreader.o recordbatchwriter.o safe-call-into-r-impl.o scalar.o schema.o symbols.o table.o threadpool.o type_infer.o -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-arrow/R-arrow/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-arrow/00new/arrow/libs
** R
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-arrow/R-arrow/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-arrow/00new/arrow/libs/arrow.so':
dlopen(/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-arrow/R-arrow/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-arrow/00new/arrow/libs/arrow.so, 6): Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx
Referenced from: /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-arrow/R-arrow/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-arrow/00new/arrow/libs/arrow.so
Expected in: dynamic lookup
Error: loading failed
Execution halted
ERROR: loading failed
```
Is this something known?
`R` 4.3.2, `gcc` 13.2.0, `arrow` 14.0.1, macOS 10.6 / ppc (_yeah, a good old one_), Macports build env (no patches from our side applied to either `arrow` or `R-arrow`).
### Component(s)
R
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "barracuda156 (via GitHub)" <gi...@apache.org>.
barracuda156 commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817306717
We _need_ to build from source. But I think you are absolutely right that the reason is that the build system was changed – which I was not aware of and did not account for. (Therefore I only looked at the end of the log without reviewing what it was doing in the earlier part.)
Apparently what we should do is to patch away or modify the configure to skip attempts to use anything pre-built (that gonna be broken on powerpc) and then fix linking stage so that flags are actually passed. The latter can be done even directly into Makevars, considering that building `R-arrow` works and only linkage fails.
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817699724
Hm interesting, if you run an R session in your prefix does `Sys.which("cmake")` work?
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "barracuda156 (via GitHub)" <gi...@apache.org>.
barracuda156 commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817699496
> Yes system cmake will be picked up as long as it is on the path or `CMAKE` is set to the path of it:
>
> ```r
>
> Sys.getenv("CMAKE"),
>
> Sys.which("cmake"),
>
> Sys.which("cmake3")
>
> ```
Then it should have been picked in my case too, perhaps, since of course it is installed and into a standard Macports prefix (some ports do use a dedicated subprefix but not CMake).
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817338068
> Just to be clear, you gonna retain an option to link to an external arrow in 15.0.0, right? That is desirable to have, at least as a non-default choice.
Yes the workaround is just due to the abseil version bump being painful in our bundled build (we use external project currently but can now use fetchcontent which will make version upgrades much easier).
Let me know if using arrow cpp 14.0.0 works to skip the bundled build :)
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "barracuda156 (via GitHub)" <gi...@apache.org>.
barracuda156 commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817301423
@assignUser Thank you for responding!
Pre-built binaries won’t do in our case, since a) it is against the policy of Macports (everything that is buildable from source should be built from source) and b) there are simply no pre-built binaries for a number of systems we support (in particular powerpc ones, likely i386, and perhaps not limited to those).
Build log:
[R-arrow_10.6_build_log.txt](https://github.com/apache/arrow/files/13398565/R-arrow_10.6_build_log.txt)
It indeed does something weird now after configure, but then still builds from source; however the build system apparently fails to pass flags to the linker (which would explain missing symbols).
P. S. I actually run it natively on a PowerMac: it is faster on G5 Quad than on my Intel machine in Rosetta.
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817308287
>Apparently what we should do is to patch away or modify the configure to skip attempts to use anything pre-built (that gonna be broken on powerpc) and then fix linking stage so that flags are actually passed.
The flags were not passed because the source build failed but for some reason didn't kill the whole package install.... I have no idea why but will look into it.
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817682867
Just to summarize the issue, there are two actual issues here causing the titular build error of this issue:
1. We download a cmake binary for the new bundled source build, for some reason this failed. (maybe because its ppc?)
2. This error should have stopped the configure script and thus cancled the package install, it did not.
3. (matching of versions might be to strict which caused the hotfixed macports 14.0.1 to be rejected)
In regards to your build setup and how to influence what libarrow isued / build:
- By default arrow uses pkg-config to look for an existing install of arrow, which did happen here to but was rejected due to the version mismatch (see 3.)
- `ARROW_HOME` can be set to an existing libarrow build (usually used in a dev context) and force that to be used, this will not be version checked, so you should be able to use that to force the use of your existing libarrow version. (or of course keep your workaround trhat patches out the version check)
- `LIBARROW_BINARY` can be used to force a build from source with `false` or enable the use of precompiled binaries (default on macos but disabled on some linux distros) with `true` but only comes into play after pc and `ARROW_HOME`
- `LIBARROW_BUILD=FALSE` can be used to explicitly disable source builds
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817309074
> machine is busy rebuilding gcc13
1. oof
2. there is currently a workaround for issues with our source build (includes an older abseil version that doesn't compile on gcc13) that disables gcs, but as you are going to use the system libarrow you can force that with `ARROW_GCS=ON` (this workaround will hopefully be removed for 15.0.0)
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "barracuda156 (via GitHub)" <gi...@apache.org>.
barracuda156 commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817679039
@paleolimbot Replying now from memory, but I think “binary”-referring arg was removed in that rewrite of configure. I can try still adding it there just to check.
As of now, building is fixed (with a minimal patch to configure – just to ensure it does not break what otherwise works).
I do think a failure handling could be improved: errors one gets now and not readable, IMO. I mean, if I do not patch anything and do not pass custom args, it should either still work correctly (like it did with 13.0.0) or at least give out a debug output pointing at the problem and failing where it is supposed to.
What happens with 14.0.0 seems like a bug: there is no reason to proceed with a build but stripping off pkgconfig flags, that just cannot work. I think 13.0.0 handled it more sensibly, but even if that is deemed undesirable now, erring out earlier with a clear error message would have prevented this issue.
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "barracuda156 (via GitHub)" <gi...@apache.org>.
barracuda156 commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817736973
@assignUser Yes it does:
```
36-158% /opt/local/bin/r
R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: powerpc-apple-darwin10.0.0d2 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.which("cmake")
cmake
"/opt/local/bin/cmake"
```
It also works fine via `R CMD`, since for example we use our CMake to build `R-nloptr`, and it gets picked normally:
https://ports.macports.org/port/R-nloptr/details
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817303962
Ah it seems to be some issue with the cmake binary that we download, I will look into that. But that's a downstream issue of this `:info:destroot **** Not using: C++ library version (14.0.1) does not match R package (14.0.0)`
14.0.0 and 14.0.1 are identical for arrow cpp (it was a hotfix release for a python only cve). So just using arrow 14.0.0 will likely already skip the build from source :)
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817307974
We are also able to use a version of arrow cpp installed on the host found via pkg-config, which as you added it tp the port file will be build from source for macports should satisfy your policy?
You can enforce a source build with `LIBARROW_BINARY=false`. Set `CMAKE` to the path of cmake (>= 3.16) to skip the part where we download a cmake binary as that seems to be broken...
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "barracuda156 (via GitHub)" <gi...@apache.org>.
barracuda156 commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817686977
@assignUser Thank you for the summary, it is clear now.
If someone builds `arrow` from within R, is it still possible without manual hackery to use an external CMake? This is not required for me (since we do not build this from within R), but thinking of any non-mainstream platform, pre-built binary gonna fail: there won’t be any CMake binaries even for 10.4 i386, forget something like Unix on mips32 or 10.5 ppc64. But there may be a pre-installed CMake on any given system.
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817698086
Yes system cmake will be picked up as long as it is on the path or `CMAKE` is set to the path of it:
```r
Sys.getenv("CMAKE"),
Sys.which("cmake"),
Sys.which("cmake3")
```
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "barracuda156 (via GitHub)" <gi...@apache.org>.
barracuda156 commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817319362
> The flags were not passed because the source build failed but for some reason didn't kill the whole package install.... I have no idea why but will look into it.
Not really sure, since in this case we do not patch anything. Here is the exact port I used (update to the earlier version, which worked with no issues with `arrow` 13.0.0): https://github.com/macports/macports-ports/commit/3411bafc22c024e7eea5e8ca18d22cc3f50c0065
I.e. from our side we only ensure the right choice of compiler (cxx_standard setting).
> there is currently a workaround for issues with our source build (includes an older abseil version that doesn't compile on gcc13) that disables gcs, but as you are going to use the system libarrow you can force that with ARROW_GCS=ON (this workaround will hopefully be removed for 15.0.0)
We would certainly prefer to avoid rebuilding `arrow` itself just for the usage in R. It is still built from source, just in a way it is available generally.
(`abseil` is a painful port, which we have to carry patches for: my PR to upstream, I think, is still hanging for ages open.)
Just to be clear, you gonna retain an option to link to an external `arrow` in 15.0.0, right? That is desirable to have, at least as a non-default choice.
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "barracuda156 (via GitHub)" <gi...@apache.org>.
barracuda156 commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817680693
P. S. Perhaps some of my replies above are a bit confusing re building or not building from source.
To be clear, what we need in Macports context:
– `apache-arrow` port is built from source, standalone (without any involvement of `R`).
– `R-arrow` port (R package) is itself built from source, but uses Macports `apache-arrow` installation (dependency is declared, so it will be required to be built prior to R package, unless already installed in Macports context).
What we would like to avoid is rebuilding a duplicate copy of `apache-arrow` exclusive to R usage (waste of compilation time and disk space), as long as using a pre-installed one works reliably. It still *could* be done, technically, but rather avoided.
What we must avoid, both for policy reasons and technical ones, is downloading anything pre-built from outside (as long as it is not something absolutely required, like a bootstrap binary for a compiler which cannot be built from source otherwise).
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser closed issue #38769: Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx`
URL: https://github.com/apache/arrow/issues/38769
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817737487
Hm, thanks for testing, not sure what the issue is but I'll look into it
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "barracuda156 (via GitHub)" <gi...@apache.org>.
barracuda156 commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817426316
@assignUser So yes, what was effectively breaking it is a version mismatch which triggered an attempt to download pre-built `arrow`, apparently, and that could not end well :)
Despite that failed, the build somehow managed to proceed, but with all flags wiped out, so nothing went to Makevars and eventually to the linker. With ldflags missing, `libarrow` were simply not found.
So you were right.
Commenting out a chunk of code which prohibits using mismatched versions fixes everything: `pkg-config` passes flags, those go to the linker:
```
*** Trying Arrow C++ found by pkg-config: /opt/local
PKG_CFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_ACERO -DARROW_R_WITH_SUBSTRAIT -DARROW_R_WITH_JSON -DARROW_R_WITH_GCS
PKG_LIBS=-L/opt/local/lib -larrow_substrait -larrow_dataset -larrow_acero -lparquet -larrow
** libs
using C++ compiler: ‘g++-mp-13 (MacPorts gcc13 13.2.0_4+stdlib_flag) 13.2.0’
using C++17
```
Package installs normally:
```
/opt/local/bin/g++-mp-13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/Library/Frameworks/R.framework/Resources/lib -Wl,-headerpad_max_install_names -Wl,-rpath,/opt/local/lib/libgcc -L/opt/local/lib -lMacportsLegacySupport -arch ppc -o arrow.so RTasks.o altrep.o array.o array_to_vector.o arraydata.o arrowExports.o bridge.o buffer.o chunkedarray.o compression.o compute-exec.o compute.o config.o csv.o dataset.o datatype.o expression.o extension-impl.o feather.o field.o filesystem.o io.o json.o memorypool.o message.o parquet.o r_to_arrow.o recordbatch.o recordbatchreader.o recordbatchwriter.o safe-call-into-r-impl.o scalar.o schema.o symbols.o table.o threadpool.o type_infer.o -L/opt/local/lib -larrow_substrait -larrow_dataset -larrow_acero -lparquet -larrow -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-arrow/R-arrow/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-arrow/00new/arrow/libs
** R
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (arrow)
```
P. S. Not really sure why this change was made; in 13.0.0 version mismatch triggered a warning (totally justified behavior), but did not break anything. Perhaps it makes sense at least to display some meaningful error, since otherwise it may not be obvious what fails, especially when it worked earlier.
It would also be helpful to have a readable error re unsupported archs: I do not expect `arrow` to provide pre-built libs for macOS PowerPC, of course, or, say, Irix, but the process fails with something unintelligible:
```
shasum: tools/checksums/darwin-power: No such file or directory
*** Checksum validation failed for libarrow binary:
```
If there are no pre-built binaries for a combo of OS and arch, perhaps let the configure script instruct to build `libarrow` manually?
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817684802
I have opened https://github.com/apache/arrow/issues/38776, https://github.com/apache/arrow/issues/38777 and https://github.com/apache/arrow/issues/38778 to adress the actual issues and will close this for now as your problem is solved for now. Please feel free to add any further comments in this issue even if it's closed :)
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "paleolimbot (via GitHub)" <gi...@apache.org>.
paleolimbot commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817588680
I think `LIBARROW_BINARY=false` or `LIBARROW_DOWNLOAD=false` should prevent the source build (apologies if you already tried that!)
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Re: [I] Linking error: `Symbol not found: __ZN5arrow12ArrayBuilder12AppendScalarERKNS_6ScalarEx` [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #38769:
URL: https://github.com/apache/arrow/issues/38769#issuecomment-1817288308
I am unfamiliar with the macports build setup but with 14.0.0 we have completely overhauled the build system for the R package under macos and windows. That is likely the source for the issue as the build on macos now uses the same system as the linux build with pre-compiled binaries or build from source if that wasn't found.
You could try to set `LIBARROW_BINARY=true` to force the use of the precompiled binaries (we have them for openssl 1.1 and 3) to skip the use of system arrow.
Do you have a CI run where I can see the complete log (specifically the bits at the beginning before the actual compilation)?
Sidenote are you cross compiling with quemu for 10.6 or how are you running such an old version?
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