[ARROW-4316] Reusing arrow.so for both Python and R

• Type: Bug
• Status: Closed
• Priority: Major
• Resolution: Duplicate
• Affects Version/s: 0.12.0
• Component/s: Python, R
• Environment: Ubuntu 16.04, R 3.4.4, pyarrow 0.12, cmake 3.12
• External issue URL: https://github.com/apache/arrow/issues/20888
• Assignee: Unassigned
• Reporter: Jeffrey Wong
• Created: 22/Jan/19 04:32
• Updated: 11/Jan/23 07:33
• Resolved: 15/Aug/19 21:03

Description

My team uses both pyarrow and R arrow, we'd like both libraries to link to the same arrow.so file for consistency. pyarrow ships both arrow.so and parquet.so, if I can reuse those .so's to  link R that would guarantee consistency. 
Under arrow v0.11.1 I was able to link R against libarrow.so found under pyarrow by passing LIB_DIR to the R configure file. However, in v0.12.0 I am no longer able to do that. Here is a reproducible example on Ubuntu 16.04 which produces the error:

 

sh: line 1: 5404 Segmentation fault (core dumped) '/usr/lib/R/bin/R' --no-save --slave 2>&1 < '/tmp/RtmpyOuz4g/file14716feda8fc'
*** caught segfault ***
address 0x7f160f026250, cause 'invalid permissions'
An irrecoverable exception occurred. R is aborting now ...

 

Reproducible example:

 # get the parquet headers which are not shipped with pyarrow
  
tee /etc/apt/sources.list.d/apache-arrow.list <<APT_LINE
deb [arch=amd64] https://dl.bintray.com/apache/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/ $(lsb_release --codename --short) main
deb-src [] https://dl.bintray.com/apache/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/ $(lsb_release --codename --short) main
APT_LINE
apt-get update
mkdir /tmp/arrow_headers; cd /tmp/arrow_headers
apt-get download --allow-unauthenticated libparquet-dev
ar -x libparquet-dev_0.12.0-1_amd64.deb
tar -xJvf data.tar.xz
  
 #get pyarrow v0.12
  
 pip3 install pyarrow --upgrade
 #figure out where pyarrow is
 PY_ARROW_PATH=$(python3 -c "import pyarrow, os; print(os.path.dirname(pyarrow.__file__))")
 PY_ARROW_VERSION=$(python3 -c "import pyarrow; print(pyarrow.__version__)")
 PYTHON_LIBDIR=$(python3 -c "import sysconfig; print(sysconfig.get_config_var('LIBDIR'))")
  

 # pyarrow doesn't ship parquet headers. Copy the ones from apt into the pyarrow dir
 mkdir $PY_ARROW_PATH/include/parquet
 cp -r /tmp/arrow_headers/usr/include/parquet/* $PY_ARROW_PATH/include/parquet/
  
 #install R arrow
 echo "export LD_LIBRARY_PATH=\"\${LD_LIBRARY_PATH}:${PYTHON_LIBDIR}:${PY_ARROW_PATH}\"" | tee -a /usr/lib/R/etc/ldpaths
 git clone https://github.com/apache/arrow.git /tmp/arrow
 cd /tmp/arrow/r
 git checkout "apache-arrow-${PY_ARROW_VERSION}"
 sed -i "/Depends: R/c\Depends: R (>= 3.4)" DESCRIPTION
 sed -i "s/PKG_CXXFLAGS=/PKG_CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 /g" src/Makevars.in
 R CMD INSTALL ./ --configure-vars="INCLUDE_DIR=$PY_ARROW_PATH/include LIB_DIR=$PY_ARROW_PATH" 

Issue Links

• is duplicated by: ARROW-5956 [R] Ability for R to link to C++ libraries from pyarrow Wheel