pyarrow appears to depend on system libxml2 #1740
Description
Solution to issue cannot be found in the documentation.
- I checked the documentation.
Issue
In a fresh Ubuntu 24.04 container with miniforge installed:
(pyarrow-test) root@a52c25fe3525:/# python
Python 3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyarrow
Traceback (most recent call last):
File "<python-input-0>", line 1, in <module>
import pyarrow
File "/root/miniforge3/envs/pyarrow-test/lib/python3.13/site-packages/pyarrow/__init__.py", line 65, in <module>
import pyarrow.lib as _lib
ImportError: libxml2.so.2: cannot open shared object file: No such file or directory
>>>
(pyarrow-test) root@a52c25fe3525:/# ldd /root/miniforge3/envs/pyarrow-test/lib/python3.13/site-packages/pyarrow/lib.cpython-313-x86_64-linux-gnu.so | grep xml
libxml2.so.2 => not found
It appears the package linked against the system libxml and not the conda-forge version.
Installed packages
# packages in environment at /root/miniforge3/envs/pyarrow-test:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aws-c-auth 0.8.7 h7743f02_1 conda-forge
aws-c-cal 0.8.7 h7d555fd_1 conda-forge
aws-c-common 0.12.1 hb9d3cd8_0 conda-forge
aws-c-compression 0.3.1 hcbd9e4e_3 conda-forge
aws-c-event-stream 0.5.4 h286e7e7_3 conda-forge
aws-c-http 0.9.5 hbca0721_0 conda-forge
aws-c-io 0.17.0 ha855f32_8 conda-forge
aws-c-mqtt 0.12.2 hffac463_3 conda-forge
aws-c-s3 0.7.13 h4c9fe3b_3 conda-forge
aws-c-sdkutils 0.2.3 hcbd9e4e_3 conda-forge
aws-checksums 0.2.3 hcbd9e4e_3 conda-forge
aws-crt-cpp 0.31.1 h46b750d_1 conda-forge
aws-sdk-cpp 1.11.510 h1fa5cb7_4 conda-forge
azure-core-cpp 1.14.0 h5cfcd09_0 conda-forge
azure-identity-cpp 1.10.0 h113e628_0 conda-forge
azure-storage-blobs-cpp 12.13.0 h3cf044e_1 conda-forge
azure-storage-common-cpp 12.8.0 h736e048_1 conda-forge
azure-storage-files-datalake-cpp 12.12.0 ha633028_1 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.4 hb9d3cd8_0 conda-forge
ca-certificates 2025.1.31 hbcca054_0 conda-forge
gflags 2.2.2 h5888daf_1005 conda-forge
glog 0.7.1 hbabe93e_0 conda-forge
icu 75.1 he02047a_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
libabseil 20250127.1 cxx17_hbbce691_0 conda-forge
libarrow 19.0.1 h052fb8e_6_cpu conda-forge
libarrow-acero 19.0.1 hcb10f89_6_cpu conda-forge
libarrow-dataset 19.0.1 hcb10f89_6_cpu conda-forge
libarrow-flight 19.0.1 hba9a014_6_cpu conda-forge
libarrow-flight-sql 19.0.1 h1bed206_6_cpu conda-forge
libarrow-gandiva 19.0.1 h8debca8_6_cpu conda-forge
libarrow-substrait 19.0.1 h1bed206_6_cpu conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_2 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_2 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_2 conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 8.13.0 h332b0f4_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.7.0 h5888daf_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libgcc 14.2.0 h767d61c_2 conda-forge
libgcc-ng 14.2.0 h69a702a_2 conda-forge
libgomp 14.2.0 h767d61c_2 conda-forge
libgoogle-cloud 2.36.0 hc4361e1_1 conda-forge
libgoogle-cloud-storage 2.36.0 h0121fbd_1 conda-forge
libgrpc 1.71.0 he753a82_0 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
libllvm18 18.1.8 default_hb5137d0_5 conda-forge
liblzma 5.8.1 hb9d3cd8_0 conda-forge
libmpdec 4.0.0 h4bc722e_0 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libopentelemetry-cpp 1.19.0 hd1b1c89_0 conda-forge
libopentelemetry-cpp-headers 1.19.0 ha770c72_0 conda-forge
libparquet 19.0.1 h081d1f1_6_cpu conda-forge
libprotobuf 5.29.3 h501fc15_0 conda-forge
libre2-11 2024.07.02 hba17884_3 conda-forge
libsqlite 3.49.1 hee588c1_2 conda-forge
libssh2 1.11.1 hf672d98_0 conda-forge
libstdcxx 14.2.0 h8f9b012_2 conda-forge
libstdcxx-ng 14.2.0 h4852527_2 conda-forge
libthrift 0.21.0 h0e7cc3e_0 conda-forge
libutf8proc 2.10.0 h4c51ac1_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxml2 2.14.0 h8d12d68_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
nlohmann_json 3.11.3 he02047a_1 conda-forge
openssl 3.4.1 h7b32b05_0 conda-forge
orc 2.1.1 h17f744e_1 conda-forge
pip 25.0.1 pyh145f28c_0 conda-forge
prometheus-cpp 1.3.0 ha5d0236_0 conda-forge
pyarrow 19.0.1 py313h78bf25f_0 conda-forge
pyarrow-all 19.0.1 py313h78bf25f_0 conda-forge
pyarrow-core 19.0.1 py313he5f92c8_0_cpu conda-forge
python 3.13.2 hf636f53_101_cp313 conda-forge
python_abi 3.13 6_cp313 conda-forge
re2 2024.07.02 h9925aae_3 conda-forge
readline 8.2 h8c095d6_2 conda-forge
s2n 1.5.15 hd830067_0 conda-forge
snappy 1.2.1 h8bd8927_1 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tzdata 2025b h78e105d_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forgeEnvironment info
mamba version : 1.5.12
active environment : pyarrow-test
active env location : /root/miniforge3/envs/pyarrow-test
shell level : 2
user config file : /root/.condarc
populated config files : /root/miniforge3/.condarc
conda version : 24.11.3
conda-build version : not installed
python version : 3.12.9.final.0
solver : libmamba (default)
virtual packages : __archspec=1=skylake
__conda=24.11.3=0
__glibc=2.39=0
__linux=6.8.0=0
__unix=0=0
base environment : /root/miniforge3 (writable)
conda av data dir : /root/miniforge3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /root/miniforge3/pkgs
/root/.conda/pkgs
envs directories : /root/miniforge3/envs
/root/.conda/envs
platform : linux-64
user-agent : conda/24.11.3 requests/2.32.3 CPython/3.12.9 Linux/6.8.0-52-generic ubuntu/24.04.1 glibc/2.39 solver/libmamba conda-libmamba-solver/24.9.0 libmambapy/1.5.12
UID:GID : 0:0
netrc file : None
offline mode : False