[jira] [Created] (ARROW-5956) Undefined symbol GetFieldByName

["Jeffrey Wong (JIRA)" <ji...@apache.org>]

Jeffrey Wong created ARROW-5956:
-----------------------------------

             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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