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Posted to jira@arrow.apache.org by "Vincent Nijs (Jira)" <ji...@apache.org> on 2022/09/03 02:03:00 UTC
[jira] [Commented] (ARROW-17374) [R] R Arrow install fails with SNAPPY_LIB-NOTFOUND
[ https://issues.apache.org/jira/browse/ARROW-17374?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17599759#comment-17599759 ]
Vincent Nijs commented on ARROW-17374:
--------------------------------------
Made some progress. I had to install `libsnappy-dev` and `libre2-dev` in Ubuntu 22.04 and use [https://github.com/duckdb/duckdb/issues/3049#issuecomment-1096671708]
Arrow still doesn't compile successfully, however, and ends with the below. The build logs are attached ("build-images.out").
```
#21 1786.1 ** testing if installed package can be loaded from temporary location
#21 1786.4 Error: package or namespace load failed for ‘arrow’ in dyn.load(file, DLLpath = DLLpath, ...):
#21 1786.4 unable to load shared object '/usr/local/lib/R/site-library/00LOCK-arrow/00new/arrow/libs/arrow.so':
#21 1786.4 /usr/local/lib/R/site-library/00LOCK-arrow/00new/arrow/libs/arrow.so: undefined symbol: _ZTIN6apache6thrift8protocol9TProtocolE
```
```
# workaround for fPIC issue [https://github.com/duckdb/duckdb/issues/3049#issuecomment-1096671708]
cp -a /usr/local/lib/R/etc/Makeconf /usr/local/lib/R/etc/Makeconf.bak;
sed -i 's/fpic/fPIC/g' /usr/local/lib/R/etc/Makeconf;
R -e "options(HTTPUserAgent = sprintf('R/%s R (%s)', getRversion(), paste(getRversion(), R.version['platform'], R.version['arch'], R.version['os']))); Sys.setenv('ARROW_R_DEV' = TRUE); install.packages(c('duckdb', 'arrow'), repo='${CRAN}', Ncpus=${NCPUS})"
mv /usr/local/lib/R/etc/Makeconf.bak /usr/local/lib/R/etc/Makeconf;
```
> [R] R Arrow install fails with SNAPPY_LIB-NOTFOUND
> --------------------------------------------------
>
> Key: ARROW-17374
> URL: https://issues.apache.org/jira/browse/ARROW-17374
> Project: Apache Arrow
> Issue Type: Bug
> Components: R
> Affects Versions: 8.0.0, 9.0.0, 8.0.1
> Environment: Amazon Linux 2 (RHEL) - 5.10.102-99.473.amzn2.x86_64
> Reporter: Shane Brennan
> Priority: Blocker
> Attachments: build-images.out
>
>
> I've been trying to install Arrow on an R notebook within AWS SageMaker. SageMaker provides Jupyter-like notebooks, with each instance running Amazon Linux 2 as its OS, itself based on RHEL.
> Trying to install a few ways, e.g., using the standard binaries, using the nightly builds, setting ARROW_WITH_SNAPPY to ON and LIBARROW_MINIMAL all still result in the following error.
> {noformat}
> x86_64-conda-linux-gnu-c++ -std=gnu++11 -shared -L/home/ec2-user/anaconda3/envs/R/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/ec2-user/anaconda3/envs/R/lib -Wl,-rpath-link,/home/ec2-user/anaconda3/envs/R/lib -L/home/ec2-user/anaconda3/envs/R/lib -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 imports.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/Rtmpuh87oc/R.INSTALL67114493a3de/arrow/libarrow/arrow-9.0.0.20220809/lib -larrow_dataset -lparquet -larrow -larrow_bundled_dependencies -lz SNAPPY_LIB-NOTFOUND /home/ec2-user/anaconda3/envs/R/lib/libbz2.so -pthread -larrow -larrow_bundled_dependencies -larrow_dataset -lparquet -lssl -lcrypto -lcurl -lssl -lcrypto -lcurl -L/home/ec2-user/anaconda3/envs/R/lib/R/lib -lR
> x86_64-conda-linux-gnu-c++: error: SNAPPY_LIB-NOTFOUND: No such file or directory
> make: *** [/home/ec2-user/anaconda3/envs/R/lib/R/share/make/shlib.mk:10: arrow.so] Error 1{noformat}
> Snappy is installed on the systems, and both shared object (.so) and cmake files are there, where I've tried setting the system env variables Snappy_DIR and Snappy_LIB to point at them, but to no avail.
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