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Posted to issues@arrow.apache.org by "gowerc (via GitHub)" <gi...@apache.org> on 2024/07/19 15:08:33 UTC
[I] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
gowerc opened a new issue, #43337:
URL: https://github.com/apache/arrow/issues/43337
### Describe the bug, including details regarding any error messages, version, and platform.
Heya,
Am currently trying to install the latest R CRAN version of arrow but keep getting the following error:
```
> install.packages("arrow")
Installing package into ‘/home/gowerc/R/x86_64-redhat-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/arrow_16.1.0.tar.gz'
Content type 'application/x-gzip' length 4439675 bytes (4.2 MB)
==================================================
downloaded 4.2 MB
* installing *source* package ‘arrow’ ...
** package ‘arrow’ successfully unpacked and MD5 sums checked
** using staged installation
*** pkg-config found.
*** Trying Arrow C++ found by pkg-config: /usr
**** Not using: C++ library version (15.0.2): not supported by R package version 16.1.0
*** Found local C++ source: 'tools/cpp'
*** Building libarrow from source
For build options and troubleshooting, see the install guide:
https://arrow.apache.org/docs/r/articles/install.html
**** cmake 3.28.2: /usr/bin/cmake
**** arrow
PKG_CFLAGS=-DUTF8PROC_EXPORTS -I/tmp/RtmpfZTpu0/R.INSTALL37cd0e2a5202/arrow/libarrow/arrow-16.1.0/include -DARROW_STATIC -DPARQUET_STATIC -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_ACERO -DARROW_R_WITH_JSON
PKG_LIBS=-L/tmp/RtmpfZTpu0/R.INSTALL37cd0e2a5202/arrow/libarrow/arrow-16.1.0/lib -lsnappy -llz4 -lutf8proc -larrow_dataset -larrow -larrow_bundled_dependencies -ldl -lparquet -larrow_acero
** libs
using C++ compiler: ‘g++ (GCC) 14.1.1 20240701 (Red Hat 14.1.1-7)’
using C++17
<lots of compiler log skipped>
** 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 '/home/gowerc/R/x86_64-redhat-linux-gnu-library/4.4/00LOCK-arrow/00new/arrow/libs/arrow.so':
/home/gowerc/R/x86_64-redhat-linux-gnu-library/4.4/00LOCK-arrow/00new/arrow/libs/arrow.so: undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/gowerc/R/x86_64-redhat-linux-gnu-library/4.4/arrow’
The downloaded source packages are in
‘/tmp/RtmpiE3fZa/downloaded_packages’
Warning message:
In install.packages("arrow") :
installation of package ‘arrow’ had non-zero exit status
```
## General Debug Information
```
> version
_
platform x86_64-redhat-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 4.1
year 2024
month 06
day 14
svn rev 86737
language R
version.string R version 4.4.1 (2024-06-14)
nickname Race for Your Life
```
```
> cat /etc/os-release
NAME="Fedora Linux"
VERSION="40 (Workstation Edition)"
ID=fedora
VERSION_ID=40
VERSION_CODENAME=""
PLATFORM_ID="platform:f40"
PRETTY_NAME="Fedora Linux 40 (Workstation Edition)"
ANSI_COLOR="0;38;2;60;110;180"
LOGO=fedora-logo-icon
CPE_NAME="cpe:/o:fedoraproject:fedora:40"
DEFAULT_HOSTNAME="fedora"
HOME_URL="https://fedoraproject.org/"
DOCUMENTATION_URL="https://docs.fedoraproject.org/en-US/fedora/f40/system-administrators-guide/"
SUPPORT_URL="https://ask.fedoraproject.org/"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Fedora"
REDHAT_BUGZILLA_PRODUCT_VERSION=40
REDHAT_SUPPORT_PRODUCT="Fedora"
REDHAT_SUPPORT_PRODUCT_VERSION=40
SUPPORT_END=2025-05-13
VARIANT="Workstation Edition"
VARIANT_ID=workstation
```
Not sure if relevant but I had installed the parquet dev lib from `dnf` for separate project:
```
> sudo dnf info parquet-libs-devel
Last metadata expiration check: 2:39:56 ago on Fri 19 Jul 2024 13:27:15 BST.
Installed Packages
Name : parquet-libs-devel
Version : 15.0.2
Release : 3.fc40
Architecture : x86_64
Size : 489 k
Source : libarrow-15.0.2-3.fc40.src.rpm
Repository : @System
From repo : fedora
Summary : Libraries and header files for Apache Parquet C++
URL : https://arrow.apache.org/
License : Apache-2.0
Description : Libraries and header files for Apache Parquet C++.
```
### Component(s)
R
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "gowerc (via GitHub)" <gi...@apache.org>.
gowerc commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2239619487
@assignUser
Thanks for the advice, I have updated the [link](https://gist.github.com/gowerc/6c96fb454fb3f002daece58888fdfe78) with the full log. Please let me know if there's anything else I can do to help debug.
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2239717135
Hm, I think this is the issue: https://gist.github.com/gowerc/6c96fb454fb3f002daece58888fdfe78#file-log-txt-L463
I guess the .so file gets lost after the package is build and installed... we probably need to enforce `ARROW_DEPENDENCY_USE_SHARED` in the build script.
We are currently working on the next CRAN release, I will investigate and make sure a patch is included cc @jonkeane
@gowerc did installing with the precompiled binary work?
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "gowerc (via GitHub)" <gi...@apache.org>.
gowerc commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2241078318
@assignUser - Just to say that running the following (as you suggested) worked for me.
```
LIBARROW_BINARY=true Rscript -e "install.packages('arrow')"
```
Thank you !!
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "gowerc (via GitHub)" <gi...@apache.org>.
gowerc commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2244682914
Thanks for looking into this !
Yup the workaround is working so hopefully the upstream will be fixed soon or at least for Fedora-41. That being said its still only listing the old version in Fedora packages at the moment 😢
https://packages.fedoraproject.org/pkgs/pkgconf/pkgconf/
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2240556315
Trying to repro this in docker now to get a fix going so we can include it in the CRAN release of 17.0.0
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "gowerc (via GitHub)" <gi...@apache.org>.
gowerc commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2240965518
You guys probably know more about CRAN submissions than me but just wanted to point out that two of the test machines on CRAN are fedora which might cause your 17.0 submission to fail.
Though frustratingly they don't use the version of GCC that is available from the package manager (assuming they've compiled it themselves)
https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-fedora-gcc
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2244013317
Thanks.
It seems that `pkgconf` in Fedora 40 has a problem:
```console
$ docker run -it --rm -v $PWD:/host fedora:40
$ dnf install -y pkgconf
$ rpm -qa | grep pkgconf
pkgconf-m4-2.1.1-1.fc40.noarch
libpkgconf-2.1.1-1.fc40.x86_64
pkgconf-2.1.1-1.fc40.x86_64
pkgconf-pkg-config-2.1.1-1.fc40.x86_64
$ PKG_CONFIG_PATH=/host/pcfiles pkgconf --libs arrow-dataset parquet
-L/tmp/Rtmpo6n7mE/R.INSTALL10001961ec66/arrow/libarrow/arrow-16.1.0/lib -larrow_dataset -larrow_acero -larrow -larrow_bundled_dependencies -ldl -lparquet
````
`-lparquet` should exist before `-larrow` but it exists at the end.
Here is a result on Debian GNU/Linux sid:
```bash
$ dpkg -l | grep pkgconf
ii libextutils-pkgconfig-perl 1.16-3 all Perl interface to the pkg-config utility
ii libpkgconf3:amd64 1.8.1-3 amd64 shared library for pkgconf
ii pkgconf:amd64 1.8.1-3 amd64 manage compile and link flags for libraries
ii pkgconf-bin 1.8.1-3 amd64 manage compile and link flags for libraries (binaries)
ii python3-pkgconfig 1.5.5-2 all Python interface to the pkg-config command line tool
$ PKG_CONFIG_PATH=/tmp/download/pcfiles pkgconf --libs arrow-dataset parquet
-L/tmp/Rtmpo6n7mE/R.INSTALL10001961ec66/arrow/libarrow/arrow-16.1.0/lib -larrow_dataset -larrow_acero -lparquet -larrow -larrow_bundled_dependencies -ldl
```
`-lparquet` exists before `-larrow`.
I also tried https://github.com/pkgconf/pkgconf master:
```bash
$ git clone git@github.com:pkgconf/pkgconf.git
$ meson setup --prefix=/tmp/local pkgconf.build pkgconf
$ ninja -C pkgconf.build
$ pkgconf.build/pkgconf --version
2.2.0
$ PKG_CONFIG_PATH=/tmp/download/pcfiles pkgconf.build/pkgconf --libs arrow-dataset parquet
-L/tmp/Rtmpo6n7mE/R.INSTALL10001961ec66/arrow/libarrow/arrow-16.1.0/lib -larrow_dataset -larrow_acero -lparquet -larrow -larrow_bundled_dependencies -ldl
```
`-lparquet` exists before `-larrow`.
It seems that `pkgconf` in Fedora 40 has a problem. https://bugzilla.redhat.com/show_bug.cgi?id=2298067 may be related.
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "gowerc (via GitHub)" <gi...@apache.org>.
gowerc commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2239490738
Sure @assignUser, please find it [here](https://gist.github.com/gowerc/6c96fb454fb3f002daece58888fdfe78).
Just to say I removed by local arrow development libraries / headers and re-ran and got the same issue so doesn't look like its anything to do with that (if that helps at all...)
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "gowerc (via GitHub)" <gi...@apache.org>.
gowerc commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2240962353
Sorry does this mean you were able to recreate the issue ? Just curious to know if it's my machine / setup Vs a more general issue
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2241297521
Can we share `arrow*.pc` and `parquet.pc`?
For example, https://gist.github.com/gowerc/6c96fb454fb3f002daece58888fdfe78#file-log-txt-L1001 is the location of `arrow.pc`. Other `*.pc` should exist in the same directory.
BTW, it's not related to this problem but it seems link order without `pkg-config` is wrong:
```diff
diff --git a/r/configure b/r/configure
index 0882ee6719..1bad59ad9d 100755
--- a/r/configure
+++ b/r/configure
@@ -347,13 +347,6 @@ add_feature_flags () {
# NOTE: parquet is assumed to have the same -L flag as arrow
# so there is no need to add its location to PKG_DIRS
fi
- if arrow_built_with ARROW_DATASET; then
- PKG_CFLAGS_FEATURES="$PKG_CFLAGS_FEATURES -DARROW_R_WITH_DATASET"
- PKG_CONFIG_NAMES_FEATURES="$PKG_CONFIG_NAMES_FEATURES arrow-dataset"
- PKG_LIBS_FEATURES_WITHOUT_PC="-larrow_dataset $PKG_LIBS_FEATURES_WITHOUT_PC"
- # NOTE: arrow_dataset is assumed to have the same -L flag as arrow
- # so there is no need to add its location to PKG_DIRS
- fi
if arrow_built_with ARROW_ACERO; then
PKG_CFLAGS_FEATURES="$PKG_CFLAGS_FEATURES -DARROW_R_WITH_ACERO"
PKG_CONFIG_NAMES_FEATURES="$PKG_CONFIG_NAMES_FEATURES arrow-acero"
@@ -361,6 +354,13 @@ add_feature_flags () {
# NOTE: arrow_acero is assumed to have the same -L flag as arrow
# so there is no need to add its location to PKG_DIRS
fi
+ if arrow_built_with ARROW_DATASET; then
+ PKG_CFLAGS_FEATURES="$PKG_CFLAGS_FEATURES -DARROW_R_WITH_DATASET"
+ PKG_CONFIG_NAMES_FEATURES="$PKG_CONFIG_NAMES_FEATURES arrow-dataset"
+ PKG_LIBS_FEATURES_WITHOUT_PC="-larrow_dataset $PKG_LIBS_FEATURES_WITHOUT_PC"
+ # NOTE: arrow_dataset is assumed to have the same -L flag as arrow
+ # so there is no need to add its location to PKG_DIRS
+ fi
if arrow_built_with ARROW_SUBSTRAIT; then
PKG_CFLAGS_FEATURES="$PKG_CFLAGS_FEATURES -DARROW_R_WITH_SUBSTRAIT"
PKG_CONFIG_NAMES_FEATURES="$PKG_CONFIG_NAMES_FEATURES arrow-substrait"
```
`libarrow_dataset` depends on `libarrow_acero`. So `-larrow_dataset -larrow_acero` order is correct.
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "david-cortes (via GitHub)" <gi...@apache.org>.
david-cortes commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2263007575
@assignUser I get the same error on debian 12 with the arrow that gets compiled on-the-fly when calling `install.packages` without any existing `libarrow` installation. The error happens whether I use `gcc` or `clang` as compiler. Albeit with `clang` it complains about a different symbol `_ZN6apache6thrift8protocol16TProtocolFactoryD2Ev`.
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2264311050
Hmm. Debian 12 doesn't use pkgconf 2.1.1: https://packages.debian.org/bookworm/pkgconf
It may be a different issue. Could you open a new issue and add your full log to it like this issue's description?
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2246320022
If you're interesting in this, how about opening a pull request like https://src.fedoraproject.org/rpms/pkgconf/pull-request/10#request_diff ?
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2244073217
Thank you for investigating and the informative code blocks @kou!
I am going to close this issue as it's not something we can fix on our end, let's hope they upgrade the version in the fedora repo to 2.2+ soon.
@gowerc You already have a workaround but if you want to build from source for some reason you can disable the use of pc via the envvar `ARROW_USE_PKG_CONFIG=false` though with the bug kou pointed out above it might also error, I will see that the patch is included in 17.0.0.
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2239496092
> (if that helps at all...)
Yes very good thank you!
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2241292568
Hmm. It seems that this is caused by wrong link order:
https://gist.github.com/gowerc/6c96fb454fb3f002daece58888fdfe78#file-log-txt-L1499
```text
g++ -std=gnu++17 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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/tmp/RtmpQmOHjc/R.INSTALL46f6c3a31d910/arrow/libarrow/arrow-16.1.0/lib -lsnappy -llz4 -lutf8proc -larrow_dataset -larrow -larrow_bundled_dependencies -ldl -lparquet -larrow_acero -L/usr/lib64/R/lib -lR
```
Here is the `-l` options part in the command line:
```text
-lsnappy
-llz4
-lutf8proc
-larrow_dataset
-larrow
-larrow_bundled_dependencies
-ldl
-lparquet
-larrow_acero
-L/usr/lib64/R/lib
-lR
```
It should be:
```text
-larrow_dataset
-lparquet
-larrow_acero
-larrow
-larrow_bundled_dependencies
-ldl
-lsnappy
-llz4
-lutf8proc
-L/usr/lib64/R/lib
-lR
```
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2243222742
Thanks @kou here are the files:
[pcfiles.tar.gz](https://github.com/user-attachments/files/16325658/pcfiles.tar.gz)
(wow I just saw today, monday, that apparently my comment was never send)
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser closed issue #43337: [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE
URL: https://github.com/apache/arrow/issues/43337
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2239476898
@gowerc could you upload the full cmake log as a gist or pastebin?
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2239517222
Could you re-run it with `ARROW_R_DEV=true` as an envvar so we get the full cmake log?
As workaround to unblock you can install with `LIBARROW_BINARY=true` that should fetch a pre-compiled binary matching your system.
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Re: [I] [R] Unable to install arrow on Fedora40 undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43337:
URL: https://github.com/apache/arrow/issues/43337#issuecomment-2240876595
Ok I think the issue is different than I thought and also happens with the above option set... maybe it is caused by gcc 14 on fedora? It doesn't seem to be a gcc 14 issue as I was able to build on ubuntu with 14 and on fedora 38 with gcc13.
I am not familiar enough with fedora to really troubleshoot this further at the moment, sorry. Though I have confirmed that `LIBARROW_BINARY=true` works, you only need to have `libcurl-devel openssl-devel` installed.
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