libgdal.so.20: undefined symbol: _ZN6kmldom5ParseERKSsPSs

[snowman2]

This is for those who may run into this issue for a pointer to the resolution.

conda:
current version: 4.5.4

Issue:

<module>
    import rasterio
  File "/opt/conda/envs/testenv/lib/python3.6/site-packages/rasterio/__init__.py", line 23, in <module>
    from rasterio._base import gdal_version
ImportError: /opt/conda/envs/testenv/lib/python3.6/site-packages/rasterio/../../../libgdal.so.20: undefined symbol: _ZN11xercesc_3_211InputSource11setEncodingEPKt

rasterio-1.0.9
libgdal-2.2.4

Related to: conda-forge/fiona-feedstock#68

[snowman2]

Ah, actually, looks like the resolution is a year old. Hmmm, must be related.

[snowman2]

Yep, definitely related. Solution: remove defaults channel

[GreatEmerald]

Same issue here, but all the packages are from conda-forge already...

[GreatEmerald]

Solution that worked for me:

conda install --channel conda-forge --override-channels "gdal>2.2.4"

i.e. use newer GDAL (that installs 2.3)

[snowman2]

Ran into this: undefined symbol: _ZN11xercesc_3_211InputSource11setEncodingEPKt

And as @GreatEmerald said, libgdal=2.3.* fixes this.

[ocefpaf]

Something may be badly pinned and hence the downgrades b/c conda tries to wiggle its way out of complex solutions. I will try to identify which one and remove it.

[MatCast]

I was having the same problem, @GreatEmerald solution worked for me too.

[mariusvniekerk]

@conda-forge-admin please rerender

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-webservice.

I've rerendered the recipe as requested, but nothing actually changed.

[jhamman]

@ocefpaf / @mariusvniekerk - the re-render on this repo didn't do anything? What's the next step towards addressing the problems described here?

[shoyer]

Does something more need to be done to cause the "re-render" to occur? I'm still seeing segfaults when rasterio is installed on readthedocs (for xarray's doc build, see pydata/xarray#2705)

[jhamman]

@shoyer and I are clearly thinking on the same wave length right now :)

[snowman2]

One thing I have noticed is that specific builds of rasterio get pinned to specific versions of GDAL. So, to use the fixed pin for libgdal, you need the most recent version of rasterio.

[ocefpaf]

@shoyer and @jhamman I'm trying to figure which version/build number of rasterio is the problematic one but I cannot find a package list for the env in https://readthedocs.org/projects/xray/builds/8443648

@snowman2 you reported rasterio-1.0.9 and libgdal-2.2.4, I can try to rebuild rasterio-1.0.9 but the latest version, rasterio-1.0.13, installs libgdal-2.4.0 and works as expected. I just tested:

conda create --name TEST --channel conda-forge python=3.7 rasterio
conda activate TEST
python -c 'import rasterio; print(rasterio.__version__)'

[snowman2]

Ah yes. The version 1.0.9 did not work. I had to use 1.0.13.

[ocefpaf]

Ah yes. The version 1.0.9 did not work. I had to use 1.0.13.

I removed that one from the main channel. Thanks!

[ocefpaf]

@snowman2 are you still experiencing this? I so please re-open but I removed the offending package and the latest updates should have taken care of that.

[snowman2]

All is good now. 👍