Jeffrey Wong created ARROW-5956:
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Summary: Undefined symbol GetFieldByName
Key: ARROW-5956
URL: https://issues.apache.org/jira/browse/ARROW-5956
Project: Apache Arrow
Issue Type: Bug
Components: R
Environment: Ubuntu 16.04, R 3.4.4, python 3.6.5
Reporter: Jeffrey Wong
I have installed pyarrow 0.14.0 and want to be able to also use R arrow. In my
work I use rpy2 a lot to exchange python data structures with R data
structures, so would like R arrow to link against the exact same .so files
found in pyarrow
When I pass in include_dir and lib_dir to R's configure, pointing to pyarrow's
include and pyarrow's root directories, I am able to compile R's arrow.so file.
However, I am unable to load it in an R session, getting the error:
{code:java}
> dyn.load('arrow.so')
Error in dyn.load("arrow.so") :
unable to load shared object '/tmp/arrow2/r/src/arrow.so':
/tmp/arrow2/r/src/arrow.so: undefined symbol:
_ZNK5arrow11StructArray14GetFieldByNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE{code}
Steps to reproduce:
Install pyarrow, which also ships libarrow.so and libparquet.so
{code:java}
pip3 install pyarrow --upgrade --user
PY_ARROW_PATH=$(python3 -c "import pyarrow, os;
print(os.path.dirname(pyarrow.__file__))")
PY_ARROW_VERSION=$(python3 -c "import pyarrow; print(pyarrow.__version__)")
ln -s $PY_ARROW_PATH/libarrow.so.14 $PY_ARROW_PATH/libarrow.so
ln -s $PY_ARROW_PATH/libparquet.so.14 $PY_ARROW_PATH/libparquet.so
{code}
Add to LD_LIBRARY_PATH
{code:java}
sudo tee -a /usr/lib/R/etc/ldpaths <<LINES
LD_LIBRARY_PATH="\${LD_LIBRARY_PATH}:$PY_ARROW_PATH"
export LD_LIBRARY_PATH
LINES
sudo tee -a /usr/lib/rstudio-server/bin/r-ldpath <<LINES
LD_LIBRARY_PATH="\${LD_LIBRARY_PATH}:$PY_ARROW_PATH"
export LD_LIBRARY_PATH
LINES
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:$PY_ARROW_PATH"
{code}
Install r arrow from source
{code:java}
git clone https://github.com/apache/arrow.git /tmp/arrow2
cd /tmp/arrow2/r
git checkout tags/apache-arrow-0.14.0
R CMD INSTALL ./ --configure-vars="INCLUDE_DIR=$PY_ARROW_PATH/include
LIB_DIR=$PY_ARROW_PATH"{code}
I have noticed that the R package for arrow no longer has an RcppExports, but
instead an arrowExports. Could it be that the lack of RcppExports has made it
difficult to find GetFieldByName?
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